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Spurgin LG, Bosse M, Adriaensen F, Albayrak T, Barboutis C, Belda E, Bushuev A, Cecere JG, Charmantier A, Cichon M, Dingemanse NJ, Doligez B, Eeva T, Erikstad KE, Fedorov V, Griggio M, Heylen D, Hille S, Hinde CA, Ivankina E, Kempenaers B, Kerimov A, Krist M, Kvist L, Laine VN, Mänd R, Matthysen E, Nager R, Nikolov BP, Norte AC, Orell M, Ouyang J, Petrova-Dinkova G, Richner H, Rubolini D, Slagsvold T, Tilgar V, Török J, Tschirren B, Vágási CI, Yuta T, Groenen MAM, Visser ME, van Oers K, Sheldon BC, Slate J. The great tit HapMap project: A continental-scale analysis of genomic variation in a songbird. Mol Ecol Resour 2024; 24:e13969. [PMID: 38747336 DOI: 10.1111/1755-0998.13969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 04/10/2024] [Accepted: 04/29/2024] [Indexed: 06/04/2024]
Abstract
A major aim of evolutionary biology is to understand why patterns of genomic diversity vary within taxa and space. Large-scale genomic studies of widespread species are useful for studying how environment and demography shape patterns of genomic divergence. Here, we describe one of the most geographically comprehensive surveys of genomic variation in a wild vertebrate to date; the great tit (Parus major) HapMap project. We screened ca 500,000 SNP markers across 647 individuals from 29 populations, spanning ~30 degrees of latitude and 40 degrees of longitude - almost the entire geographical range of the European subspecies. Genome-wide variation was consistent with a recent colonisation across Europe from a South-East European refugium, with bottlenecks and reduced genetic diversity in island populations. Differentiation across the genome was highly heterogeneous, with clear 'islands of differentiation', even among populations with very low levels of genome-wide differentiation. Low local recombination rates were a strong predictor of high local genomic differentiation (FST), especially in island and peripheral mainland populations, suggesting that the interplay between genetic drift and recombination causes highly heterogeneous differentiation landscapes. We also detected genomic outlier regions that were confined to one or more peripheral great tit populations, probably as a result of recent directional selection at the species' range edges. Haplotype-based measures of selection were related to recombination rate, albeit less strongly, and highlighted population-specific sweeps that likely resulted from positive selection. Our study highlights how comprehensive screens of genomic variation in wild organisms can provide unique insights into spatio-temporal evolutionary dynamics.
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Affiliation(s)
- Lewis G Spurgin
- School of Biological Sciences, Norwich Research Park, University of East Anglia, Norwich, UK
- Department of Biology, Edward Grey Institute, University of Oxford, Oxford, UK
| | - Mirte Bosse
- Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
- Animal Breeding and Genomics, Wageningen University and Research, Wageningen, The Netherlands
- Department of Ecological Science, Animal Ecology Group, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Frank Adriaensen
- Evolutionary Ecology Group, Department of Biology, University of Antwerp, Antwerp, Belgium
| | - Tamer Albayrak
- Department of Biology, Science and art Faculty, Mehmet Akif Ersoy University, Istiklal Yerleskesi, Burdur, Turkey
- Biology Education, Buca Faculty of Education, Mathematics and Science Education, Dokuz Eylül University, İzmir, Turkey
| | | | - Eduardo Belda
- Institut d'Investigació per a la Gestió Integrada de Zones Costaneres, Campus de Gandia, Universitat Politècnica de València, València, Spain
| | - Andrey Bushuev
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Jacopo G Cecere
- Area Avifauna Migratrice, Istituto Superiore per la Protezione e la Ricerca Ambientale (ISPRA), Ozzano Emilia, Italy
| | | | - Mariusz Cichon
- Institute of Environmental Sciences, Jagiellonian University, Kraków, Poland
| | - Niels J Dingemanse
- Behavioural Ecology, Faculty of Biology, LMU München, Planegg-Martinsried, Germany
| | - Blandine Doligez
- UMR CNRS 5558-LBBE, Biométrie et Biologie Évolutive, Villeurbanne, France
- Department of Ecology and Evolution, Animal Ecology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Tapio Eeva
- Department of Biology, University of Turku, Turku, Finland
| | - Kjell Einar Erikstad
- Norwegian Institute for Nature Research, FRAM-High North Research Centre for Climate and the Environment, Tromsø, Norway
| | | | - Matteo Griggio
- Department of Biology, University of Padova, Padova, Italy
| | - Dieter Heylen
- Department of Biology, Edward Grey Institute, University of Oxford, Oxford, UK
- Evolutionary Ecology Group, Department of Biology, University of Antwerp, Antwerp, Belgium
- Interuniversity Institute for Biostatistics and Statistical Bioinformatics, Hasselt University, Diepenbeek, Belgium
| | - Sabine Hille
- Institute of Wildlife Biology and Game Management, University of Natural Resources and Life Science, Vienna, Austria
| | - Camilla A Hinde
- Behavioural Ecology Group, Department of Life Sciences, Anglia Ruskin University, Cambridgeshire, UK
| | - Elena Ivankina
- Faculty of Biology, Zvenigorod Biological Station, Lomonosov Moscow State University, Moscow, Russia
| | - Bart Kempenaers
- Department of Ornithology, Max Planck Institute for Biological Intelligence, Seewiesen, Germany
| | - Anvar Kerimov
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Milos Krist
- Department of Zoology, Faculty of Science, Palacký University, Olomouc, Czech Republic
| | - Laura Kvist
- Department of Ecology and Genetics, University of Oulu, Oulu, Finland
| | - Veronika N Laine
- Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
- Zoology Unit, Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
| | - Raivo Mänd
- Department of Zoology, University of Tartu, Tartu, Estonia
| | - Erik Matthysen
- Evolutionary Ecology Group, Department of Biology, University of Antwerp, Antwerp, Belgium
| | - Ruedi Nager
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, Glasgow, UK
| | - Boris P Nikolov
- Bulgarian Ornithological Centre, Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Ana Claudia Norte
- MARE - Marine and Environmental Sciences Centre, Department of Life Sciences, Faculty of Sciences and Technology, University of Coimbra, Coimbra, Portugal
| | - Markku Orell
- Department of Ecology and Genetics, University of Oulu, Oulu, Finland
| | | | - Gergana Petrova-Dinkova
- Bulgarian Ornithological Centre, Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Heinz Richner
- Evolutionary Ecology Lab, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Diego Rubolini
- Dipartimento di Scienze e Politiche Ambientali, Università Degli Studi di Milano, Milan, Italy
| | - Tore Slagsvold
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Vallo Tilgar
- Department of Zoology, University of Tartu, Tartu, Estonia
| | - János Török
- Behavioural Ecology Group, Department of Systematic Zoology and Ecology, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Barbara Tschirren
- Centre for Ecology and Conservation, University of Exeter, Penryn, UK
| | - Csongor I Vágási
- Evolutionary Ecology Group, Hungarian Department of Biology and Ecology, Babeș-Bolyai University, Cluj-Napoca, Romania
| | - Teru Yuta
- Yamashina Institute for Ornithology, Abiko, Japan
| | - Martien A M Groenen
- Animal Breeding and Genomics, Wageningen University and Research, Wageningen, The Netherlands
| | - Marcel E Visser
- Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
- Animal Breeding and Genomics, Wageningen University and Research, Wageningen, The Netherlands
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, Groningen, the Netherlands
| | - Kees van Oers
- Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
| | - Ben C Sheldon
- Department of Biology, Edward Grey Institute, University of Oxford, Oxford, UK
| | - Jon Slate
- School of Biosciences, University of Sheffield, Sheffield, UK
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Rebhun RB, York D, De Graaf FMD, Yoon P, Batcher KL, Luker ME, Ryan S, Peyton J, Kent MS, Stern JA, Bannasch DL. A variant in the 5'UTR of ERBB4 is associated with lifespan in Golden Retrievers. GeroScience 2024; 46:2849-2862. [PMID: 37855863 PMCID: PMC11009206 DOI: 10.1007/s11357-023-00968-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 09/29/2023] [Indexed: 10/20/2023] Open
Abstract
Genome-wide association studies (GWAS) in long-lived human populations have led to identification of variants associated with Alzheimer's disease and cardiovascular disease, the latter being the most common cause of mortality in people worldwide. In contrast, naturally occurring cancer represents the leading cause of death in pet dogs, and specific breeds like the Golden Retriever (GR) carry up to a 65% cancer-related death rate. We hypothesized that GWAS of long-lived GRs might lead to the identification of genetic variants capable of modifying longevity within this cancer-predisposed breed. A GWAS was performed comparing GR dogs ≥ 14 years to dogs dying prior to age 12 which revealed a significant association to ERBB4, the only member of the epidermal growth factor receptor family capable of serving as both a tumor suppressor gene and an oncogene. No coding variants were identified, however, distinct haplotypes in the 5'UTR were associated with reduced lifespan in two separate populations of GR dogs. When all GR dogs were analyzed together (n = 304), the presence of haplotype 3 was associated with shorter survival (11.8 years vs. 12.8 years, p = 0.024). GRs homozygous for haplotype 3 had the shortest survival, and GRs homozygous for haplotype 1 had the longest survival (11.6 years vs. 13.5 years, p = 0.0008). Sub-analyses revealed that the difference in lifespan for GRs carrying at least 1 copy of haplotype 3 was specific to female dogs (p = 0.009), whereas survival remained significantly different in both male and female GRs homozygous for haplotype 1 or haplotype 3 (p = 0.026 and p = 0.009, respectively). Taken together, these findings implicate a potential role for ERBB4 in GR longevity and provide evidence that within-breed canine lifespan studies could serve as a mechanism to identify favorable or disease-modifying variants important to the axis of aging and cancer.
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Affiliation(s)
- Robert B Rebhun
- Department of Surgical and Radiological Sciences, University of California, Davis, CA, USA.
| | - Daniel York
- Department of Surgical and Radiological Sciences, University of California, Davis, CA, USA
| | - Flora M D De Graaf
- Department of Population Health and Reproduction, University of California, Davis, CA, USA
| | - Paula Yoon
- Veterinary Medical Teaching Hospital, University of California, Davis, CA, USA
| | - Kevin L Batcher
- Department of Population Health and Reproduction, University of California, Davis, CA, USA
| | - Madison E Luker
- Department of Surgical and Radiological Sciences, University of California, Davis, CA, USA
| | - Stephanie Ryan
- Department of Population Health and Reproduction, University of California, Davis, CA, USA
| | - Jamie Peyton
- Veterinary Medical Teaching Hospital, University of California, Davis, CA, USA
| | - Michael S Kent
- Department of Surgical and Radiological Sciences, University of California, Davis, CA, USA
| | - Joshua A Stern
- Department of Medicine and Epidemiology, University of California, Davis, CA, USA
| | - Danika L Bannasch
- Department of Population Health and Reproduction, University of California, Davis, CA, USA.
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da Fonseca IIM, Nagamine MK, Gentile LB, Nishiya AT, da Fonseca JM, de Oliveira Massoco C, Ward JM, Liu S, Leppla SH, Dagli MLZ. Targeting canine mammary neoplastic epithelial cells with a reengineered anthrax toxin: first study. Vet Res Commun 2024:10.1007/s11259-024-10400-5. [PMID: 38805149 DOI: 10.1007/s11259-024-10400-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 04/29/2024] [Indexed: 05/29/2024]
Abstract
Mammary tumors are the most frequent type of neoplasms in intact female dogs. New therapies that target neoplastic cells without affecting normal cells are highly sought. The Bacillus anthracis toxin has been reengineered to target tumor cells that express urokinase plasminogen activators and metalloproteinases. In previous studies carried out in our laboratory, the reengineered anthrax toxin had inhibitory effects on canine oral mucosal melanoma and canine osteosarcoma cells. In this study, five canine neoplastic epithelial cell lines (four adenocarcinomas and one adenoma) and one non-neoplastic canine mammary epithelial cell line were treated with different concentrations of reengineered anthrax toxin components. Cell viability was quantified using an MTT assay and half-maximal inhibitory concentration (IC50) values. Cell lines were considered sensitive when the IC50 was lower than 5000 ng/ml. One canine mammary adenocarcinoma cell line and one mammary adenoma cell line showed significantly decreased viability after treatment, whereas the non-neoplastic cell line was resistant. We conclude that the reengineered anthrax toxin may be considered a targeted therapy for canine mammary neoplasms while preserving normal canine mammary epithelial cells.
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Affiliation(s)
- Ivone Izabel Mackowiak da Fonseca
- Department of Pathology, School of Veterinary Medicine and Animal Science, University of Sao Paulo, São Paulo, SP, 05508-270, Brazil
| | - Márcia Kazumi Nagamine
- Department of Pathology, School of Veterinary Medicine and Animal Science, University of Sao Paulo, São Paulo, SP, 05508-270, Brazil
| | - Luciana Boffoni Gentile
- Department of Pathology, School of Veterinary Medicine and Animal Science, University of Sao Paulo, São Paulo, SP, 05508-270, Brazil
| | - Adriana Tomoko Nishiya
- Department of Pathology, School of Veterinary Medicine and Animal Science, University of Sao Paulo, São Paulo, SP, 05508-270, Brazil
| | - Jonathan Mackowiak da Fonseca
- Department of Pathology, School of Veterinary Medicine and Animal Science, University of Sao Paulo, São Paulo, SP, 05508-270, Brazil
| | - Cristina de Oliveira Massoco
- Department of Pathology, School of Veterinary Medicine and Animal Science, University of Sao Paulo, São Paulo, SP, 05508-270, Brazil
| | | | - Shihui Liu
- Aging Institute and Division of Infectious Diseases, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Stephen Howard Leppla
- Microbial Pathogenesis Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Maria Lucia Zaidan Dagli
- Department of Pathology, School of Veterinary Medicine and Animal Science, University of Sao Paulo, São Paulo, SP, 05508-270, Brazil.
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4
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Filippo D, Guardone L, Listorti V, Elisabetta R. Microbiome in cancer: A comparative analysis between humans and dogs. Vet J 2024; 305:106145. [PMID: 38788999 DOI: 10.1016/j.tvjl.2024.106145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 04/22/2024] [Accepted: 05/21/2024] [Indexed: 05/26/2024]
Abstract
Cancer is a major cause of death in humans and animals worldwide. While cancer survival rates have increased over recent decades, further research to identify risk factors for the onset and progression of disease, and safe and highly efficacious treatments, is needed. Spontaneous tumours in pets represent an excellent model for neoplastic disease in humans. In this regard, dogs are an interesting species, as the divergence between the dog and human genome is low, humans and dogs have important similarities in the development and functioning of the immune system, and both species often share the same physical environment. There is also a higher homology between the canine and human microbiome than murine model. This review aims to describe and organize recently published information on canine microbiome assemblages and their relationship with the onset and progression of colorectal cancer, breast cancer and lymphoma, and to compare this with human disease. In both species, dysbiosis can induce variations in the gut microbiota that strongly influence shifts in status between health and disease. This can produce an inflammatory state, potentially leading to neoplasia, especially in the intestine, thus supporting canine studies in comparative oncology. Intestinal dysbiosis can also alter the efficacy and side effects of cancer treatments. Fewer published studies are available on changes in the relevant microbiomes in canine lymphoma and mammary cancer, and further research in this area could improve our understanding of the role of microbiota in the development of these cancers.
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Affiliation(s)
- Dell'Anno Filippo
- National Reference Center of Veterinary and Comparative Oncology (CEROVEC), Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d'Aosta, Genova 16129, Italy; Department of Public Health, Experimental and Forensic Medicine, Section of Biostatistics and Clinical Epidemiology, University of Pavia, Pavia, Italy
| | - Lisa Guardone
- National Reference Center of Veterinary and Comparative Oncology (CEROVEC), Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d'Aosta, Genova 16129, Italy
| | - Valeria Listorti
- National Reference Center of Veterinary and Comparative Oncology (CEROVEC), Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d'Aosta, Genova 16129, Italy
| | - Razzuoli Elisabetta
- National Reference Center of Veterinary and Comparative Oncology (CEROVEC), Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d'Aosta, Genova 16129, Italy.
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5
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Parker HG, Harris AC, Plassais J, Dhawan D, Kim EM, Knapp DW, Ostrander EA. Genome-wide analyses reveals an association between invasive urothelial carcinoma in the Shetland sheepdog and NIPAL1. NPJ Precis Oncol 2024; 8:112. [PMID: 38778091 PMCID: PMC11111773 DOI: 10.1038/s41698-024-00591-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 04/14/2024] [Indexed: 05/25/2024] Open
Abstract
Naturally occurring canine invasive urinary carcinoma (iUC) closely resembles human muscle invasive bladder cancer in terms of histopathology, metastases, response to therapy, and low survival rate. The heterogeneous nature of the disease has led to the association of large numbers of risk loci in humans, however most are of small effect. There exists a need for new and accurate animal models of invasive bladder cancer. In dogs, distinct breeds show markedly different rates of iUC, thus presenting an opportunity to identify additional risk factors and overcome the locus heterogeneity encountered in human mapping studies. In the association study presented here, inclusive of 100 Shetland sheepdogs and 58 dogs of other breeds, we identify a homozygous protein altering point mutation within the NIPAL1 gene which increases risk by eight-fold (OR = 8.42, CI = 3.12-22.71), accounting for nearly 30% of iUC risk in the Shetland sheepdog. Inclusion of six additional loci accounts for most of the disease risk in the breed and explains nearly 75% of the phenotypes in this study. When combined with sequence data from tumors, we show that variation in the MAPK signaling pathway is an overarching cause of iUC susceptibility in dogs.
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Affiliation(s)
- Heidi G Parker
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Center, National Institutes of Health, Bethesda, MD, USA
| | - Alexander C Harris
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Center, National Institutes of Health, Bethesda, MD, USA
| | - Jocelyn Plassais
- Institut de Génétique et Développement de Rennes, CNRS-UMR6290, University of Rennes, 35000, Rennes, France
| | - Deepika Dhawan
- Department of Veterinary Clinical Sciences, College of Veterinary Medicine, Purdue University, West Lafayette, IN, USA
| | - Erika M Kim
- Center for Biomedical Informatics & Information Technology, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - Deborah W Knapp
- Department of Veterinary Clinical Sciences, College of Veterinary Medicine, Purdue University, West Lafayette, IN, USA
- Purdue University Center for Cancer Research, West Lafayette, IN, USA
| | - Elaine A Ostrander
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Center, National Institutes of Health, Bethesda, MD, USA.
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Muscatello LV, Gobbo F, Avallone G, Innao M, Benazzi C, D'Annunzio G, Romaniello D, Orioles M, Lauriola M, Sarli G. PDL1 immunohistochemistry in canine neoplasms: Validation of commercial antibodies, standardization of evaluation, and scoring systems. Vet Pathol 2024; 61:393-401. [PMID: 37920996 DOI: 10.1177/03009858231209410] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2023]
Abstract
Immuno-oncology research has brought to light the paradoxical role of immune cells in the induction and elimination of cancer. Programmed cell death protein 1 (PD1), expressed by tumor-infiltrating lymphocytes, and programmed cell death ligand 1 (PDL1), expressed by tumor cells, are immune checkpoint proteins that regulate the antitumor adaptive immune response. This study aimed to validate commercially available PDL1 antibodies in canine tissue and then, applying standardized methods and scoring systems used in human pathology, evaluate PDL1 immunopositivity in different types of canine tumors. To demonstrate cross-reactivity, a monoclonal antibody (22C3) and polyclonal antibody (cod. A1645) were tested by western blot. Cross-reactivity in canine tissue cell extracts was observed for both antibodies; however, the polyclonal antibody (cod. A1645) demonstrated higher signal specificity. Canine tumor histotypes were selected based on the human counterparts known to express PDL1. Immunohistochemistry was performed on 168 tumors with the polyclonal anti-PDL1 antibody. Only membranous labeling was considered positive. PDL1 labeling was detected both in neoplastic and infiltrating immune cells. The following tumors were immunopositive: melanomas (17 of 17; 100%), renal cell carcinomas (4 of 17; 24%), squamous cell carcinomas (3 of 17; 18%), lymphomas (2 of 14; 14%), urothelial carcinomas (2 of 18; 11%), pulmonary carcinomas (2 of 20; 10%), and mammary carcinomas (1 of 31; 3%). Gastric (0 of 10; 0%) and intestinal carcinomas (0 of 24; 0%) were negative. The findings of this study suggest that PDL1 is expressed in some canine tumors, with high prevalence in melanomas.
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Affiliation(s)
| | | | | | | | | | - Giulia D'Annunzio
- University of Bologna, Bologna, Italy
- Experimental Zooprophylactic Institute of Lombardia and Emilia-Romagna, Brescia, Italy
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Chon E, Hendricks W, White M, Rodrigues L, Haworth D, Post G. Precision Medicine in Veterinary Science. Vet Clin North Am Small Anim Pract 2024; 54:501-521. [PMID: 38212188 DOI: 10.1016/j.cvsm.2023.12.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2024]
Abstract
Precision medicine focuses on the clinical management of the individual patient, not on population-based findings. Successes from human precision medicine inform veterinary oncology. Early evidence of success for canines shows how precision medicine can be integrated into practice. Decreasing genomic profiling costs will allow increased utilization and subsequent improvement of knowledge base from which to make better informed decisions. Utility of precision medicine in canine oncology will only increase for improved cancer characterization, enhanced therapy selection, and overall more successful management of canine cancer. As such, practitioners are called to interpret and leverage precision medicine reports for their patients.
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Affiliation(s)
- Esther Chon
- Vidium Animal Health, 7201 East Henkel Way, Suite 210, Scottsdale, AZ 85255, USA
| | - William Hendricks
- Vidium Animal Health, 7201 East Henkel Way, Suite 210, Scottsdale, AZ 85255, USA
| | - Michelle White
- OneHealthCompany, Inc, 530 Lytton Avenue, 2nd Floor, Palo Alto, CA 94301, USA
| | - Lucas Rodrigues
- OneHealthCompany, Inc, 530 Lytton Avenue, 2nd Floor, Palo Alto, CA 94301, USA
| | - David Haworth
- Vidium Animal Health, 7201 East Henkel Way, Suite 210, Scottsdale, AZ 85255, USA
| | - Gerald Post
- OneHealthCompany, Inc, 530 Lytton Avenue, 2nd Floor, Palo Alto, CA 94301, USA.
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8
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Blake JM, Thompson J, HogenEsch H, Ekenstedt KJ. Heritability and genome-wide association study of vaccine-induced immune response in Beagles: A pilot study. Vaccine 2024; 42:3099-3106. [PMID: 38604911 PMCID: PMC11144447 DOI: 10.1016/j.vaccine.2024.03.076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 03/22/2024] [Accepted: 03/29/2024] [Indexed: 04/13/2024]
Abstract
Both genetic and non-genetic factors contribute to individual variation in the immune response to vaccination. Understanding how genetic background influences variation in both magnitude and persistence of vaccine-induced immunity is vital for improving vaccine development and identifying possible causes of vaccine failure. Dogs provide a relevant biomedical model for investigating mammalian vaccine genetics; canine breed structure and long linkage disequilibrium simplify genetic studies in this species compared to humans. The objective of this study was to estimate the heritability of the antibody response to vaccination against viral and bacterial pathogens, and to identify genes driving variation of the immune response to vaccination in Beagles. Sixty puppies were immunized following a standard vaccination schedule with an attenuated combination vaccine containing antigens for canine adenovirus type 2, canine distemper virus, canine parainfluenza virus, canine parvovirus, and four strains of Leptospira bacteria. Serum antibody measurements for each viral and bacterial component were measured at multiple time points. Heritability estimations and GWAS were conducted using SNP genotypes at 279,902 markers together with serum antibody titer phenotypes. The heritability estimates were: (1) to Leptospira antigens, ranging from 0.178 to 0.628; and (2) to viral antigens, ranging from 0.199 to 0.588. There was not a significant difference between overall heritability of vaccine-induced immune response to Leptospira antigens compared to viral antigens. Genetic architecture indicates that SNPs of low to high effect contribute to immune response to vaccination. GWAS identified two genetic markers associated with vaccine-induced immune response phenotypes. Collectively, these findings indicate that genetic regulation of the immune response to vaccination is antigen-specific and influenced by multiple genes of small effect.
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Affiliation(s)
- Jeanna M Blake
- Department of Basic Medical Sciences, College of Veterinary Medicine, Purdue University, West Lafayette, IN, USA.
| | - James Thompson
- Zoetis, Veterinary Medicine Research and Development, Kalamazoo, MI, USA
| | - Harm HogenEsch
- Department of Comparative Pathobiology, College of Veterinary Medicine, Purdue University, West Lafayette, IN, USA; Purdue Institute of Inflammation, Immunology and Infectious Diseases, West Lafayette, IN, USA
| | - Kari J Ekenstedt
- Department of Basic Medical Sciences, College of Veterinary Medicine, Purdue University, West Lafayette, IN, USA
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9
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Sadiq S, Holmes EC, Mahar JE. Genomic and phylogenetic features of the Picobirnaviridae suggest microbial rather than animal hosts. Virus Evol 2024; 10:veae033. [PMID: 38756987 PMCID: PMC11096803 DOI: 10.1093/ve/veae033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 03/27/2024] [Accepted: 04/18/2024] [Indexed: 05/18/2024] Open
Abstract
The RNA virus family Picobirnaviridae has traditionally been associated with the gastrointestinal systems of terrestrial mammals and birds, with the majority of viruses detected in animal stool samples. Metatranscriptomic studies of vertebrates, invertebrates, microbial communities, and environmental samples have resulted in an enormous expansion of the genomic and phylogenetic diversity of this family. Yet picobirnaviruses remain poorly classified, with only one genus and three species formally ratified by the International Committee of Virus Taxonomy. Additionally, an inability to culture picobirnaviruses in a laboratory setting or isolate them in animal tissue samples, combined with the presence of bacterial genetic motifs in their genomes, suggests that these viruses may represent RNA bacteriophage rather than being associated with animal infection. Utilising a data set of 2,286 picobirnaviruses sourced from mammals, birds, reptiles, fish, invertebrates, microbial communities, and environmental samples, we identified seven consistent phylogenetic clusters likely representing Picobirnavirus genera that we tentatively name 'Alpha-', 'Beta-', 'Gamma-', 'Delta-', 'Epsilon-', 'Zeta-', and 'Etapicobirnavirus'. A statistical analysis of topological congruence between virus-host phylogenies revealed more frequent cross-species transmission than any other RNA virus family. In addition, bacterial ribosomal binding site motifs were more enriched in Picobirnavirus genomes than in the two groups of established RNA bacteriophage-the Leviviricetes and Cystoviridae. Overall, our findings support the hypothesis that the Picobirnaviridae have bacterial hosts and provide a lower-level taxonomic classification for this highly diverse and ubiquitous family of RNA viruses.
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Affiliation(s)
- Sabrina Sadiq
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Edward C Holmes
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
- Laboratory of Data Discovery for Health Limited, Hong Kong, SAR, China
| | - Jackie E Mahar
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
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10
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Dhein ES, Heikkilä U, Oevermann A, Blatter S, Meier D, Hartnack S, Guscetti F. Incidence rates of the most common canine tumors based on data from the Swiss Canine Cancer Registry (2008 to 2020). PLoS One 2024; 19:e0302231. [PMID: 38635572 PMCID: PMC11025767 DOI: 10.1371/journal.pone.0302231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 03/29/2024] [Indexed: 04/20/2024] Open
Abstract
Monitoring neoplasms in standardized registries facilitates epidemiologic studies of risk factors for tumor development and predisposition. In an observational study, we determined incidence rates (IR) and malignant tumor incidence rate ratios (IRR) by age, sex, and breed in Swiss dogs using demographic data from the official Swiss dog registration database Amicus. The dataset analyzed included 54'986 tumors diagnosed by histology and cytology in four Swiss veterinary pathology laboratories between 2008 and 2020. Diagnoses were coded according to the Vet-ICD-O-canine-1 system. Most tumors occurred in the skin (n = 19'045; 34.64%), soft tissues (n = 11'092; 20.17%), and mammary glands (n = 7'974; 14.50%). The IRs for all and for malignant tumors were 775/100'000 dog-years at risk (95%CI 764-777) and 338/100'000 dog-years at risk (95%CI 333-342), respectively. Females (850; 95%CI 834-853) had a higher overall tumor IR than males (679; 95%CI 666-684). The highest tumor IR was found at 11 years of age (1'857; 95%CI 1'780-1'867). Potential novel breed-specific predispositions were uncovered, with high IRs for several benign and malignant tumors in Polski Owczarek Nizinnys (overall IR: 3'303; 95%CI 2'502-3'864) and high IRs for malignant tumors in Russian Black Terriers (melanomas: 345; 95%CI 138-708), Field Spaniels (adenocarcinomas: 376; CI95% 138-817), Dogo Argentinos (mast cell tumors: 844; CI95% 591-1'169), King Charles Spaniels and Manchester Terriers (lymphomas: 319; CI95% 137-627 and 302; CI95% 98-704, respectively), Landseers (osteosarcomas: 74; CI95% 15-216), Bouvier des Flandres (hemangiosarcomas: 127; CI95% 26-371), and Bearded Collies and Cane Corso Italianos (gliomas: 91; CI95% 45-162 and 34; CI95% 7-99, respectively). Nordic hunting dogs had the highest (8.08; CI95% 3.55-16.7) and Chihuahueno the lowest cancer IRRs (0.42; 95%CI 0.31-0.57) compared to mixed breeds. In conclusion, the calculated IRs and IRRs revealed previously unknown predisposing factors, including novel breed-specific susceptibilities. The results may have implications for cancer screening, diagnostic work-up, breeding management and oncologic and translational research.
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Affiliation(s)
- Elena Sophie Dhein
- Institute of Veterinary Pathology, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | | | - Anna Oevermann
- Department of Clinical Research and Veterinary Public Health, Division of Neurological Sciences, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Sohvi Blatter
- Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Daniela Meier
- Zyto/Histo Diagnostik Labor Freienstein, Freienstein, Switzerland
| | - Sonja Hartnack
- Section of Epidemiology, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Franco Guscetti
- Institute of Veterinary Pathology, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
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11
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Armstrong EE, Bissell KL, Fatima HS, Heikkinen MA, Jessup A, Junaid MO, Lee DH, Lieb EC, Liem JT, Martin EM, Moreno M, Otgonbayar K, Romans BW, Royar K, Adler MB, Needle DB, Harkess A, Kelley JL, Mooney JA, Mychajliw AM. Chromosome-level assembly of the gray fox (Urocyon cinereoargenteus) confirms the basal loss of PRDM9 in Canidae. G3 (BETHESDA, MD.) 2024; 14:jkae034. [PMID: 38366575 PMCID: PMC10989890 DOI: 10.1093/g3journal/jkae034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 01/31/2024] [Accepted: 02/02/2024] [Indexed: 02/18/2024]
Abstract
Reference genome assemblies have been created from multiple lineages within the Canidae family; however, despite its phylogenetic relevance as a basal genus within the clade, there is currently no reference genome for the gray fox (Urocyon cinereoargenteus). Here, we present a chromosome-level assembly for the gray fox (U. cinereoargenteus), which represents the most contiguous, non-domestic canid reference genome available to date, with 90% of the genome contained in just 34 scaffolds and a contig N50 and scaffold N50 of 59.4 and 72.9 Megabases, respectively. Repeat analyses identified an increased number of simple repeats relative to other canids. Based on mitochondrial DNA, our Vermont sample clusters with other gray fox samples from the northeastern United States and contains slightly lower levels of heterozygosity than gray foxes on the west coast of California. This new assembly lays the groundwork for future studies to describe past and present population dynamics, including the delineation of evolutionarily significant units of management relevance. Importantly, the phylogenetic position of Urocyon allows us to verify the loss of PRDM9 functionality in the basal canid lineage, confirming that pseudogenization occurred at least 10 million years ago.
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Affiliation(s)
- Ellie E Armstrong
- School of Biological Sciences, Washington State University, Pullman, WA 99164, USA
| | - Ky L Bissell
- Department of Biology, Middlebury College, Middlebury, VT 05753, USA
| | - H Sophia Fatima
- Department of Biology, Middlebury College, Middlebury, VT 05753, USA
| | - Maya A Heikkinen
- Department of Biology, Middlebury College, Middlebury, VT 05753, USA
| | - Anika Jessup
- Department of Biology, Middlebury College, Middlebury, VT 05753, USA
| | - Maryam O Junaid
- Department of Biology, Middlebury College, Middlebury, VT 05753, USA
| | - Dong H Lee
- Department of Biology, Middlebury College, Middlebury, VT 05753, USA
| | - Emily C Lieb
- Department of Biology, Middlebury College, Middlebury, VT 05753, USA
| | - Josef T Liem
- Department of Biology, Middlebury College, Middlebury, VT 05753, USA
| | - Estelle M Martin
- Department of Biology, Middlebury College, Middlebury, VT 05753, USA
| | - Mauricio Moreno
- Department of Biology, Middlebury College, Middlebury, VT 05753, USA
| | | | - Betsy W Romans
- Department of Biology, Middlebury College, Middlebury, VT 05753, USA
| | - Kim Royar
- Vermont Department of Fish and Wildlife, Montpelier, VT 05620, USA
| | - Mary Beth Adler
- Vermont Department of Fish and Wildlife, Montpelier, VT 05620, USA
| | - David B Needle
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, NH 03824, USA
| | - Alex Harkess
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Joanna L Kelley
- School of Biological Sciences, Washington State University, Pullman, WA 99164, USA
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Jazlyn A Mooney
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA 90007, USA
| | - Alexis M Mychajliw
- Department of Biology, Middlebury College, Middlebury, VT 05753, USA
- Program in Environmental Studies, Middlebury College, Middlebury, VT 05753, USA
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12
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Kieler IN, Persson SM, Hagman R, Marinescu VD, Hedhammar Å, Strandberg E, Lindblad-Toh K, Arendt ML. Genome wide association study in Swedish Labrador retrievers identifies genetic loci associated with hip dysplasia and body weight. Sci Rep 2024; 14:6090. [PMID: 38480780 PMCID: PMC10937653 DOI: 10.1038/s41598-024-56060-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 03/01/2024] [Indexed: 03/17/2024] Open
Abstract
Genome wide association studies (GWAS) have been utilized to identify genetic risk loci associated with both simple and complex inherited disorders. Here, we performed a GWAS in Labrador retrievers to identify genetic loci associated with hip dysplasia and body weight. Hip dysplasia scores were available for 209 genotyped dogs. We identified a significantly associated locus for hip dysplasia on chromosome 24, with three equally associated SNPs (p = 4.3 × 10-7) in complete linkage disequilibrium located within NDRG3, a gene which in humans has been shown to be differentially expressed in osteoarthritic joint cartilage. Body weight, available for 85 female dogs, was used as phenotype for a second analysis. We identified two significantly associated loci on chromosome 10 (p = 4.5 × 10-7) and chromosome 31 (p = 2.5 × 10-6). The most associated SNPs within these loci were located within the introns of the PRKCE and CADM2 genes, respectively. PRKCE has been shown to play a role in regulation of adipogenesis whilst CADM2 has been associated with body weight in multiple human GWAS. In summary, we identified credible candidate loci explaining part of the genetic inheritance for hip dysplasia and body weight in Labrador retrievers with strong candidate genes in each locus previously implicated in the phenotypes investigated.
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Affiliation(s)
- Ida Nordang Kieler
- Department of Veterinary Clinical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Sofia Malm Persson
- Department for Breeding and Health, Swedish Kennel Club, Stockholm, Sweden
| | - Ragnvi Hagman
- Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Voichita D Marinescu
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
- SciLifeLab, Uppsala, Sweden
| | - Åke Hedhammar
- Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Erling Strandberg
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Kerstin Lindblad-Toh
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
- SciLifeLab, Uppsala, Sweden
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Maja Louise Arendt
- Department of Veterinary Clinical Sciences, University of Copenhagen, Copenhagen, Denmark.
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden.
- SciLifeLab, Uppsala, Sweden.
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13
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Moawad AS, Wang F, Zheng Y, Chen C, Saleh AA, Hou J, Song C. Evolution of Endogenous Retroviruses in the Subfamily of Caprinae. Viruses 2024; 16:398. [PMID: 38543763 PMCID: PMC10975924 DOI: 10.3390/v16030398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 02/28/2024] [Accepted: 03/01/2024] [Indexed: 05/23/2024] Open
Abstract
The interest in endogenous retroviruses (ERVs) has been fueled by their impact on the evolution of the host genome. In this study, we used multiple pipelines to conduct a de novo exploration and annotation of ERVs in 13 species of the Caprinae subfamily. Through analyses of sequence identity, structural organization, and phylogeny, we defined 28 ERV groups within Caprinae, including 19 gamma retrovirus groups and 9 beta retrovirus groups. Notably, we identified four recent and potentially active groups prevalent in the Caprinae genomes. Additionally, our investigation revealed that most long noncoding genes (lncRNA) and protein-coding genes (PC) contain ERV-derived sequences. Specifically, we observed that ERV-derived sequences were present in approximately 75% of protein-coding genes and 81% of lncRNA genes in sheep. Similarly, in goats, ERV-derived sequences were found in approximately 74% of protein-coding genes and 75% of lncRNA genes. Our findings lead to the conclusion that the majority of ERVs in the Caprinae genomes can be categorized as fossils, representing remnants of past retroviral infections that have become permanently integrated into the genomes. Nevertheless, the identification of the Cap_ERV_20, Cap_ERV_21, Cap_ERV_24, and Cap_ERV_25 groups indicates the presence of relatively recent and potentially active ERVs in these genomes. These particular groups may contribute to the ongoing evolution of the Caprinae genome. The identification of putatively active ERVs in the Caprinae genomes raises the possibility of harnessing them for future genetic marker development.
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Affiliation(s)
- Ali Shoaib Moawad
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (A.S.M.); (Y.Z.); (C.C.); (A.A.S.)
- Department of Animal Production, Faculty of Agriculture, Kafrelsheikh University, Kafrelsheikh 33516, Egypt
| | - Fengxu Wang
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, Beijing 100193, China; (F.W.); (J.H.)
| | - Yao Zheng
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (A.S.M.); (Y.Z.); (C.C.); (A.A.S.)
| | - Cai Chen
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (A.S.M.); (Y.Z.); (C.C.); (A.A.S.)
| | - Ahmed A. Saleh
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (A.S.M.); (Y.Z.); (C.C.); (A.A.S.)
- Animal and Fish Production Department, Faculty of Agriculture (Alshatby), Alexandria University, Alexandria City 11865, Egypt
| | - Jian Hou
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, Beijing 100193, China; (F.W.); (J.H.)
| | - Chengyi Song
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (A.S.M.); (Y.Z.); (C.C.); (A.A.S.)
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14
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Abrams KL, Ward DA, Sabiniewicz A, Hummel T. Olfaction evaluation in dogs with sudden acquired retinal degeneration syndrome. Vet Ophthalmol 2024; 27:127-138. [PMID: 37399129 DOI: 10.1111/vop.13121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 06/05/2023] [Accepted: 06/09/2023] [Indexed: 07/05/2023]
Abstract
PURPOSE To evaluate olfaction in dogs with sudden acquired retinal degeneration syndrome (SARDS) compared with sighted dogs and blind dogs without SARDS as control groups. ANIMALS STUDIED Forty client-owned dogs. PROCEDURE Olfactory threshold testing was performed on three groups: SARDS, sighted, and blind/non-SARDS using eugenol as the test odorant. The olfactory threshold was determined when subjects indicated the detection of a specific eugenol concentration with behavioral responses. Olfactory threshold, age, body weight, and environmental room factors were evaluated. RESULTS Sixteen dogs with SARDS, 12 sighted dogs, and 12 blind/non-SARDS dogs demonstrated mean olfactory threshold pen numbers of 2.8 (SD = 1.4), 13.8 (SD = 1.4), and 13.4 (SD = 1.1), respectively, which correspond to actual mean concentrations of 0.017 g/mL, 1.7 × 10-13 g/mL and 4.26 × 10-13 g/mL, respectively. Dogs with SARDS had significantly poorer olfactory threshold scores compared with the two control groups (p < .001), with no difference between the control groups (p = .5). Age, weight, and room environment did not differ between the three groups. CONCLUSIONS Dogs with SARDS have severely decreased olfaction capabilities compared with sighted dogs and blind/non-SARDS dogs. This finding supports the suspicion that SARDS is a systemic disease causing blindness, endocrinopathy, and hyposmia. Since the molecular pathways are similar in photoreceptors, olfactory receptors, and steroidogenesis with all using G-protein coupled receptors in the cell membrane, the cause of SARDS may exist at the G-protein associated interactions with intracellular cyclic nucleotides. Further investigations into G-protein coupled receptors pathway and canine olfactory receptor genes in SARDS patients may be valuable in revealing the cause of SARDS.
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Affiliation(s)
- Kenneth L Abrams
- Veterinary Ophthalmology Services, North Kingstown, Rhode Island, USA
| | - Daniel A Ward
- Department of Small Animal Clinical Sciences, College of Veterinary Medicine, University of Tennessee, Knoxville, Tennessee, USA
| | - Agnieszka Sabiniewicz
- Department of Otorhinolaryngology, Smell and Taste Clinic, Technische Universität Dresden, Dresden, Germany
- Institute of Psychology, University of Wrocław, Wrocław, Poland
| | - Thomas Hummel
- Department of Otorhinolaryngology, Smell and Taste Clinic, Technische Universität Dresden, Dresden, Germany
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15
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Kehl A, Aupperle-Lellbach H, de Brot S, van der Weyden L. Review of Molecular Technologies for Investigating Canine Cancer. Animals (Basel) 2024; 14:769. [PMID: 38473154 DOI: 10.3390/ani14050769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 02/09/2024] [Accepted: 02/27/2024] [Indexed: 03/14/2024] Open
Abstract
Genetic molecular testing is starting to gain traction as part of standard clinical practice for dogs with cancer due to its multi-faceted benefits, such as potentially being able to provide diagnostic, prognostic and/or therapeutic information. However, the benefits and ultimate success of genomic analysis in the clinical setting are reliant on the robustness of the tools used to generate the results, which continually expand as new technologies are developed. To this end, we review the different materials from which tumour cells, DNA, RNA and the relevant proteins can be isolated and what methods are available for interrogating their molecular profile, including analysis of the genetic alterations (both somatic and germline), transcriptional changes and epigenetic modifications (including DNA methylation/acetylation and microRNAs). We also look to the future and the tools that are currently being developed, such as using artificial intelligence (AI) to identify genetic mutations from histomorphological criteria. In summary, we find that the molecular genetic characterisation of canine neoplasms has made a promising start. As we understand more of the genetics underlying these tumours and more targeted therapies become available, it will no doubt become a mainstay in the delivery of precision veterinary care to dogs with cancer.
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Affiliation(s)
- Alexandra Kehl
- Laboklin GmbH & Co. KG, Steubenstr. 4, 97688 Bad Kissingen, Germany
- School of Medicine, Institute of Pathology, Technical University of Munich, Trogerstr. 18, 81675 München, Germany
| | - Heike Aupperle-Lellbach
- Laboklin GmbH & Co. KG, Steubenstr. 4, 97688 Bad Kissingen, Germany
- School of Medicine, Institute of Pathology, Technical University of Munich, Trogerstr. 18, 81675 München, Germany
| | - Simone de Brot
- Institute of Animal Pathology, COMPATH, University of Bern, 3012 Bern, Switzerland
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16
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Abrar M, Ali S, Hussain I, Khatoon H, Batool F, Ghazanfar S, Corcoran D, Kawakami Y, Abbasi AA. Cis-regulatory control of mammalian Trps1 gene expression. JOURNAL OF EXPERIMENTAL ZOOLOGY. PART B, MOLECULAR AND DEVELOPMENTAL EVOLUTION 2024. [PMID: 38369890 DOI: 10.1002/jez.b.23246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 12/22/2023] [Accepted: 01/31/2024] [Indexed: 02/20/2024]
Abstract
TRPS1 serves as the causative gene for tricho-rhino phalangeal syndrome, known for its craniofacial and skeletal abnormalities. The Trps1 gene encodes a protein that represses Wnt signaling through strong interactions with Wnt signaling inhibitors. The identification of genomic cis-acting regulatory sequences governing Trps1 expression is crucial for understanding its role in embryogenesis. Nevertheless, to date, no investigations have been conducted concerning these aspects of Trps1. To identify deeply conserved noncoding elements (CNEs) within the Trps1 locus, we employed a comparative genomics approach, utilizing slowly evolving fish such as coelacanth and spotted gar. These analyses resulted in the identification of eight CNEs in the intronic region of the Trps1 gene. Functional characterization of these CNEs in zebrafish revealed their regulatory potential in various tissues, including pectoral fins, heart, and pharyngeal arches. RNA in-situ hybridization experiments revealed concordance between the reporter expression pattern induced by the identified set of CNEs and the spatial expression pattern of the trps1 gene in zebrafish. Comparative in vivo data from zebrafish and mice for CNE7/hs919 revealed conserved functions of these enhancers. Each of these eight CNEs was further investigated in cell line-based reporter assays, revealing their repressive potential. Taken together, in vivo and in vitro assays suggest a context-dependent dual functionality for the identified set of Trps1-associated CNE enhancers. This functionally characterized set of CNE-enhancers will contribute to a more comprehensive understanding of the developmental roles of Trps1 and can aid in the identification of noncoding DNA variants associated with human diseases.
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Affiliation(s)
- Muhammad Abrar
- National Center for Bioinformatics, Program of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Shahid Ali
- National Center for Bioinformatics, Program of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
- Department of Organismal Biology and Anatomy, The University of Chicago, Chicago, Illinois, USA
| | - Irfan Hussain
- National Center for Bioinformatics, Program of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
- Center of Regenerative Medicine and Stem Cells Research, Aga Khan University Hospital, Karachi, Pakistan
| | - Hizran Khatoon
- National Center for Bioinformatics, Program of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Fatima Batool
- National Center for Bioinformatics, Program of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Shakira Ghazanfar
- National Institute for Genomics Advanced Biotechnology, National Agriculture Research Centre (NARC), Islamabad, Pakistan
| | - Dylan Corcoran
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, Minnesota, USA
| | - Yasuhiko Kawakami
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, Minnesota, USA
| | - Amir Ali Abbasi
- National Center for Bioinformatics, Program of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
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17
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Zhang C, Zhang S, Tian Z, Wang Y, Xu S, Wang D. Comprehensive Analysis of Phylogenetic Relationship and Optimal Codons in Mitochondrial Genomes of the Genus Pseudogastromyzon. Animals (Basel) 2024; 14:495. [PMID: 38338138 PMCID: PMC10854560 DOI: 10.3390/ani14030495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 12/20/2023] [Accepted: 01/29/2024] [Indexed: 02/12/2024] Open
Abstract
As indicator organisms for water pollution detection, Pseudogasteromyzon species play a vital role in aquatic environment monitoring. We have successfully sequenced the mitogenomes of P. fasciatus jiulongjiangensis and P. myersi and downloaded the mitogenomes of nine other Pseudogastromyzon fish on GenBank to conduct a detailed comparative analysis of their phylogenetic relationships and evolutionary history. The findings revealed a conservation in both gene composition and gene order. Except for the trnS1 gene lacking dihydrouracil arms, the other 21 tRNAs showed the typical clover-leaf secondary structure. According to the ΔRSCU method, we identified the seven most abundant optimal codons: CUA, GUA, CCA, CAA, GAA, AGC, and GGC. The construction of maximum parsimony, maximum likelihood, and Bayes trees yielded congruent topologies, and the 11 Pseudogastromyzon species were clustered into two major clusters. Among them, one of which was composed of P. fangi, P. changtingensis changtingensis, and P. changtingensis tungpeiensis, while the remaining eight species formed another cluster, further subdivided into five smaller clusters. Distinct clusters formed between P. fasciatus jiulongjiangensis and P. meihuashanensis, P. cheni and P. peristictus, and P. laticeps and P. lianjiangensis, and the remaining two species were clustered separately, thereby enhancing our understanding of them. Furthermore, our analysis results of divergence times revealed that these 11 Pseudogasteromyzon species underwent rapid differentiation in the Pleistocene epochs. Overall, our study sheds light on the phylogenetic relationship and evolutionary history of Pseudogasteromyzon species, providing a necessary knowledge foundation for further understanding the intricacies of an ecosystem health assessment.
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Affiliation(s)
- Cheng Zhang
- School of Marine Science, Ningbo University, Ningbo 315211, China; (C.Z.)
- National Engineering Research Laboratory of Marine Biotechnology and Engineering, Ningbo University, Ningbo 315211, China
| | - Shun Zhang
- School of Marine Science, Ningbo University, Ningbo 315211, China; (C.Z.)
| | - Zhe Tian
- School of Marine Science, Ningbo University, Ningbo 315211, China; (C.Z.)
| | - Yajun Wang
- School of Marine Science, Ningbo University, Ningbo 315211, China; (C.Z.)
| | - Shanliang Xu
- School of Marine Science, Ningbo University, Ningbo 315211, China; (C.Z.)
- National Engineering Research Laboratory of Marine Biotechnology and Engineering, Ningbo University, Ningbo 315211, China
| | - Danli Wang
- School of Marine Science, Ningbo University, Ningbo 315211, China; (C.Z.)
- National Engineering Research Laboratory of Marine Biotechnology and Engineering, Ningbo University, Ningbo 315211, China
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18
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Smeds L, Huson LSA, Ellegren H. Structural genomic variation in the inbred Scandinavian wolf population contributes to the realized genetic load but is positively affected by immigration. Evol Appl 2024; 17:e13652. [PMID: 38333557 PMCID: PMC10848878 DOI: 10.1111/eva.13652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 01/08/2024] [Accepted: 01/16/2024] [Indexed: 02/10/2024] Open
Abstract
When populations decrease in size and may become isolated, genomic erosion by loss of diversity from genetic drift and accumulation of deleterious mutations is likely an inevitable consequence. In such cases, immigration (genetic rescue) is necessary to restore levels of genetic diversity and counteract inbreeding depression. Recent work in conservation genomics has studied these processes focusing on the genetic diversity of single nucleotide polymorphisms. In contrast, our knowledge about structural genomic variation (insertions, deletions, duplications and inversions) in endangered species is limited. We analysed whole-genome, short-read sequences from 212 wolves from the inbred Scandinavian population and from neighbouring populations in Finland and Russia, and detected >35,000 structural variants (SVs) after stringent quality and genotype frequency filtering; >26,000 high-confidence variants remained after manual curation. The majority of variants were shorter than 1 kb, with a distinct peak in the length distribution of deletions at 190 bp, corresponding to insertion events of SINE/tRNA-Lys elements. The site frequency spectrum of SVs in protein-coding regions was significantly shifted towards rare alleles compared to putatively neutral variants, consistent with purifying selection. The realized genetic load of SVs in protein-coding regions increased with inbreeding levels in the Scandinavian population, but immigration provided a genetic rescue effect by lowering the load and reintroducing ancestral alleles at loci fixed for derived SVs. Our study shows that structural variation comprises a common type of in part deleterious mutations in endangered species and that establishing gene flow is necessary to mitigate the negative consequences of loss of diversity.
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Affiliation(s)
- Linnéa Smeds
- Department of Ecology and Genetics, Evolutionary BiologyUppsala UniversityUppsalaSweden
| | - Lars S. A. Huson
- Department of Ecology and Genetics, Evolutionary BiologyUppsala UniversityUppsalaSweden
| | - Hans Ellegren
- Department of Ecology and Genetics, Evolutionary BiologyUppsala UniversityUppsalaSweden
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19
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Vaidhya A, Ghildiyal K, Rajawat D, Nayak SS, Parida S, Panigrahi M. Relevance of pharmacogenetics and pharmacogenomics in veterinary clinical practice: A review. Anim Genet 2024; 55:3-19. [PMID: 37990577 DOI: 10.1111/age.13376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 07/03/2023] [Accepted: 10/24/2023] [Indexed: 11/23/2023]
Abstract
The recent advances in high-throughput next-generation sequencing technologies have heralded the arrival of the Big Data era. As a result, the use of pharmacogenetics in drug discovery and individualized drug therapy has transformed the field of precision medicine. This paradigm shift in drug development programs has effectively reshaped the old drug development practices, which were primarily concerned with the physiological status of patients for drug development. Pharmacogenomics bridges the gap between pharmacodynamics and pharmacokinetics, advancing current diagnostic and treatment strategies and enabling personalized and targeted drug therapy. The primary goals of pharmacogenetic studies are to improve drug efficacy and minimize toxicities, to identify novel drug targets, to estimate drug dosage for personalized medicine, and to incorporate it as a routine diagnostic for disease susceptibility. Although pharmacogenetics has numerous applications in individualized drug therapy and drug development, it is in its infancy in veterinary medicine. The objective of this review is to present an overview of historical landmarks, current developments in various animal species, challenges and future perspectives of genomics in drug development and dosage optimization for individualized medicine in veterinary subjects.
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Affiliation(s)
- Ayushi Vaidhya
- Division of Pharmacology & Toxicology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, UP, India
| | - Kanika Ghildiyal
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly, UP, India
| | - Divya Rajawat
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly, UP, India
| | - Sonali Sonejita Nayak
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly, UP, India
| | - Subhashree Parida
- Division of Pharmacology & Toxicology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, UP, India
| | - Manjit Panigrahi
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly, UP, India
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20
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vonHoldt BM, Stahler DR, Brzeski KE, Musiani M, Peterson R, Phillips M, Stephenson J, Laudon K, Meredith E, Vucetich JA, Leonard JA, Wayne RK. Demographic history shapes North American gray wolf genomic diversity and informs species' conservation. Mol Ecol 2024; 33:e17231. [PMID: 38054561 DOI: 10.1111/mec.17231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 11/19/2023] [Accepted: 11/21/2023] [Indexed: 12/07/2023]
Abstract
Effective population size estimates are critical information needed for evolutionary predictions and conservation decisions. This is particularly true for species with social factors that restrict access to breeding or experience repeated fluctuations in population size across generations. We investigated the genomic estimates of effective population size along with diversity, subdivision, and inbreeding from 162,109 minimally filtered and 81,595 statistically neutral and unlinked SNPs genotyped in 437 grey wolf samples from North America collected between 1986 and 2021. We found genetic structure across North America, represented by three distinct demographic histories of western, central, and eastern regions of the continent. Further, grey wolves in the northern Rocky Mountains have lower genomic diversity than wolves of the western Great Lakes and have declined over time. Effective population size estimates revealed the historical signatures of continental efforts of predator extermination, despite a quarter century of recovery efforts. We are the first to provide molecular estimates of effective population size across distinct grey wolf populations in North America, which ranged between Ne ~ 275 and 3050 since early 1980s. We provide data that inform managers regarding the status and importance of effective population size estimates for grey wolf conservation, which are on average 5.2-9.3% of census estimates for this species. We show that while grey wolves fall above minimum effective population sizes needed to avoid extinction due to inbreeding depression in the short term, they are below sizes predicted to be necessary to avoid long-term risk of extinction.
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Affiliation(s)
- Bridgett M vonHoldt
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, USA
| | - Daniel R Stahler
- Yellowstone Center for Resources, Yellowstone National Park, Wyoming, USA
| | - Kristin E Brzeski
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, Michigan, USA
| | - Marco Musiani
- Dipartimento di Scienze Biologiche, Geologiche e Ambientali (BiGeA), Università di Bologna, Bologna, Italy
| | - Rolf Peterson
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, Michigan, USA
| | | | | | - Kent Laudon
- California Department of Fish and Wildlife, Northern Region, Redding, California, USA
| | - Erin Meredith
- California Department of Fish and Wildlife, Wildlife Forensic Laboratory, Sacramento, California, USA
| | - John A Vucetich
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, Michigan, USA
| | - Jennifer A Leonard
- Conservation and Evolutionary Genetics Group, Estación Biológica de Doñana (EBD-CSIC), Seville, Spain
| | - Robert K Wayne
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, California, USA
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21
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Watabe T, Yamahira S, Takakura K, Thumkeo D, Narumiya S, Matsuda M, Terai K. Calcium transients trigger switch-like discharge of prostaglandin E 2 in an extracellular signal-regulated kinase-dependent manner. eLife 2024; 12:RP86727. [PMID: 38276879 PMCID: PMC10945702 DOI: 10.7554/elife.86727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2024] Open
Abstract
Prostaglandin E2 (PGE2) is a key player in a plethora of physiological and pathological events. Nevertheless, little is known about the dynamics of PGE2 secretion from a single cell and its effect on the neighboring cells. Here, by observing confluent Madin-Darby canine kidney (MDCK) epithelial cells expressing fluorescent biosensors, we demonstrate that calcium transients in a single cell cause PGE2-mediated radial spread of PKA activation (RSPA) in neighboring cells. By in vivo imaging, RSPA was also observed in the basal layer of the mouse epidermis. Experiments with an optogenetic tool revealed a switch-like PGE2 discharge in response to the increasing cytoplasmic Ca2+ concentrations. The cell density of MDCK cells correlated with the frequencies of calcium transients and the following RSPA. The extracellular signal-regulated kinase (ERK) activation also enhanced the frequency of RSPA in MDCK and in vivo. Thus, the PGE2 discharge is regulated temporally by calcium transients and ERK activity.
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Affiliation(s)
- Tetsuya Watabe
- Research Center for Dynamic Living Systems, Graduate School of Biostudies, Kyoto UniversityKyotoJapan
- Department of Pathology and Biology of Diseases, Graduate School of Medicine, Kyoto UniversityKyotoJapan
| | - Shinya Yamahira
- Research Center for Dynamic Living Systems, Graduate School of Biostudies, Kyoto UniversityKyotoJapan
| | - Kanako Takakura
- Research Center for Dynamic Living Systems, Graduate School of Biostudies, Kyoto UniversityKyotoJapan
| | - Dean Thumkeo
- Department of Drug Discovery Medicine, Graduate School of Medicine, Kyoto UniversityKyotoJapan
| | - Shuh Narumiya
- Department of Drug Discovery Medicine, Graduate School of Medicine, Kyoto UniversityKyotoJapan
| | - Michiyuki Matsuda
- Research Center for Dynamic Living Systems, Graduate School of Biostudies, Kyoto UniversityKyotoJapan
- Department of Pathology and Biology of Diseases, Graduate School of Medicine, Kyoto UniversityKyotoJapan
- Institute for Integrated Cell-Material Sciences, Kyoto UniversityKyotoJapan
| | - Kenta Terai
- Department of Pathology and Biology of Diseases, Graduate School of Medicine, Kyoto UniversityKyotoJapan
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22
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Wragg D, Zhang W, Peterson S, Yerramilli M, Mellanby R, Schoenebeck JJ, Clements DN. A cautionary tale of low-pass sequencing and imputation with respect to haplotype accuracy. Genet Sel Evol 2024; 56:6. [PMID: 38216889 PMCID: PMC10785484 DOI: 10.1186/s12711-024-00875-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 01/03/2024] [Indexed: 01/14/2024] Open
Abstract
BACKGROUND Low-pass whole-genome sequencing and imputation offer significant cost savings, enabling substantial increases in sample size and statistical power. This approach is particularly promising in livestock breeding, providing an affordable means of screening individuals for deleterious alleles or calculating genomic breeding values. Consequently, it may also be of value in companion animal genomics to support pedigree breeding. We sought to evaluate in dogs the impact of low coverage sequencing and reference-guided imputation on genotype concordance and association analyses. RESULTS DNA isolated from saliva of 30 Labrador retrievers was sequenced at low (0.9X and 3.8X) and high (43.5X) coverage, and down-sampled from 43.5X to 9.6X and 17.4X. Genotype imputation was performed using a diverse reference panel (1021 dogs), and two subsets of the former panel (256 dogs each) where one had an excess of Labrador retrievers relative to other breeds. We observed little difference in imputed genotype concordance between reference panels. Association analyses for a locus acting as a disease proxy were performed using single-marker (GEMMA) and haplotype-based (XP-EHH) tests. GEMMA results were highly correlated (r ≥ 0.97) between 43.5X and ≥ 3.8X depths of coverage, while for 0.9X the correlation was lower (r ≤ 0.8). XP-EHH results were less well correlated, with r ranging from 0.58 (0.9X) to 0.88 (17.4X). Across a random sample of 10,000 genomic regions averaging 17 kb in size, we observed a median of three haplotypes per dog across the sequencing depths, with 5% of the regions returning more than eight haplotypes. Inspection of one such region revealed genotype and phasing inconsistencies across sequencing depths. CONCLUSIONS We demonstrate that saliva-derived canine DNA is suitable for whole-genome sequencing, highlighting the feasibility of client-based sampling. Low-pass sequencing and imputation require caution as incorrect allele assignments result when the subject possesses alleles that are absent in the reference panel. Larger panels have the capacity for greater allelic diversity, which should reduce the potential for imputation error. Although low-pass sequencing can accurately impute allele dosage, we highlight issues with phasing accuracy that impact haplotype-based analyses. Consequently, if accurately phased genotypes are required for analyses, we advocate sequencing at high depth (> 20X).
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Affiliation(s)
- David Wragg
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG, UK.
| | - Wengang Zhang
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG, UK
| | - Sarah Peterson
- IDEXX Laboratories Inc, One IDEXX Drive, Westbrook, ME, 04092, USA
| | | | - Richard Mellanby
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG, UK
- IDEXX Laboratories Inc, One IDEXX Drive, Westbrook, ME, 04092, USA
| | - Jeffrey J Schoenebeck
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG, UK.
| | - Dylan N Clements
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG, UK
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23
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Tsukamoto M, Kimura K, Yoshida T, Tanaka M, Kuwamura M, Ayabe T, Ishihara G, Watanabe K, Okada M, Iijima M, Nakanishi M, Akutsu H, Sugiura K, Hatoya S. Generation of canine induced pluripotent stem cells under feeder-free conditions using Sendai virus vector encoding six canine reprogramming factors. Stem Cell Reports 2024; 19:141-157. [PMID: 38134923 PMCID: PMC10828825 DOI: 10.1016/j.stemcr.2023.11.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 11/27/2023] [Accepted: 11/27/2023] [Indexed: 12/24/2023] Open
Abstract
Although it is in its early stages, canine induced pluripotent stem cells (ciPSCs) hold great potential for innovative translational research in regenerative medicine, developmental biology, drug screening, and disease modeling. However, almost all ciPSCs were generated from fibroblasts, and available canine cell sources for reprogramming are still limited. Furthermore, no report is available to generate ciPSCs under feeder-free conditions because of their low reprogramming efficiency. Here, we reanalyzed canine pluripotency-associated genes and designed canine LIN28A, NANOG, OCT3/4, SOX2, KLF4, and C-MYC encoding Sendai virus vector, called 159cf. and 162cf. We demonstrated that not only canine fibroblasts but also canine urine-derived cells, which can be isolated using a noninvasive and straightforward method, were successfully reprogrammed with or without feeder cells. ciPSCs existed in undifferentiated states, differentiating into the three germ layers in vitro and in vivo. We successfully generated ciPSCs under feeder-free conditions, which can promote studies in veterinary and consequently human regenerative medicines.
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Affiliation(s)
- Masaya Tsukamoto
- Department of Advanced Pathobiology, Graduate School of Veterinary Science, Osaka Metropolitan University, Izumisano, Osaka 598-8531, Japan; Department of Advanced Pathobiology, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Izumisano, Osaka 598-8531, Japan; Center for Regenerative Medicine, National Center for Child Health and Development, Setagaya, Tokyo 157-8535, Japan
| | - Kazuto Kimura
- Department of Advanced Pathobiology, Graduate School of Veterinary Science, Osaka Metropolitan University, Izumisano, Osaka 598-8531, Japan; Department of Advanced Pathobiology, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Izumisano, Osaka 598-8531, Japan
| | - Takumi Yoshida
- Department of Advanced Pathobiology, Graduate School of Veterinary Science, Osaka Metropolitan University, Izumisano, Osaka 598-8531, Japan; Department of Advanced Pathobiology, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Izumisano, Osaka 598-8531, Japan
| | - Miyuu Tanaka
- Department of Integrated Structural Biosciences, Graduate School of Veterinary Science, Osaka Metropolitan University, Izumisano, Osaka 598-8531, Japan; Department of Integrated Structural Biosciences, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Izumisano, Osaka 598-8531, Japan
| | - Mitsuru Kuwamura
- Department of Integrated Structural Biosciences, Graduate School of Veterinary Science, Osaka Metropolitan University, Izumisano, Osaka 598-8531, Japan; Department of Integrated Structural Biosciences, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Izumisano, Osaka 598-8531, Japan
| | - Taro Ayabe
- Anicom Specialty Medical Institute, Shinjuku-ku, Tokyo 231-0033, Japan
| | - Genki Ishihara
- Anicom Specialty Medical Institute, Shinjuku-ku, Tokyo 231-0033, Japan
| | - Kei Watanabe
- Anicom Specialty Medical Institute, Shinjuku-ku, Tokyo 231-0033, Japan
| | - Mika Okada
- TOKIWA-Bio, Tsukuba, Ibaraki 305-0047, Japan
| | | | | | - Hidenori Akutsu
- Center for Regenerative Medicine, National Center for Child Health and Development, Setagaya, Tokyo 157-8535, Japan
| | - Kikuya Sugiura
- Department of Advanced Pathobiology, Graduate School of Veterinary Science, Osaka Metropolitan University, Izumisano, Osaka 598-8531, Japan; Department of Advanced Pathobiology, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Izumisano, Osaka 598-8531, Japan
| | - Shingo Hatoya
- Department of Advanced Pathobiology, Graduate School of Veterinary Science, Osaka Metropolitan University, Izumisano, Osaka 598-8531, Japan; Department of Advanced Pathobiology, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Izumisano, Osaka 598-8531, Japan.
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24
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Ukawa H, Akiyama N, Yamamoto F, Ohashi K, Ishihara G, Matsumoto Y. Negative Selection on a SOD1 Mutation Limits Canine Degenerative Myelopathy While Avoiding Inbreeding. Genome Biol Evol 2024; 16:evad231. [PMID: 38109923 PMCID: PMC10773665 DOI: 10.1093/gbe/evad231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 11/30/2023] [Accepted: 12/10/2023] [Indexed: 12/20/2023] Open
Abstract
Several hundred disease-causing mutations are currently known in domestic dogs. Breeding management is therefore required to minimize their spread. Recently, genetic methods such as direct-to-consumer testing have gained popularity; however, their effects on dog populations are unclear. Here, we aimed to evaluate the influence of genetic testing on the frequency of mutations responsible for canine degenerative myelopathy and assess the changes in the genetic structure of a Pembroke Welsh corgi population from Japan. Genetic testing of 5,512 dogs for the causative mutation in superoxide dismutase 1 (SOD1) (c.118G>A (p.E40K)) uncovered a recent decrease in frequency, plummeting from 14.5% (95/657) in 2019 to 2.9% (24/820) in 2022. Weir and Cockerham population differentiation (FST) based on genome-wide single-nucleotide polymorphism (SNP) of 117 selected dogs detected the SNP with the highest FST located in the intron of SOD1 adjacent to the c.118G>A mutation, supporting a selection signature on SOD1. Further genome-wide SNP analyses revealed no obvious changes in inbreeding levels and genetic diversity between the 2019 and 2022 populations. Our study highlights that genetic testing can help inform improved mating choices in breeding programs to reduce the frequency of risk variants and avoid inbreeding. This combined strategy could decrease the genetic risk of canine degenerative myelopathy, a fatal disease, within only a few years.
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Affiliation(s)
- Hisashi Ukawa
- Genetic Testing Section, Anicom Pafe Inc., Kanagawa, Japan
| | - Noriyoshi Akiyama
- Genetic Testing Section, Anicom Pafe Inc., Kanagawa, Japan
- Research and Development Section, Anicom Specialty Medical Institute Inc., Kanagawa, Japan
| | | | - Ken Ohashi
- Genetic Testing Section, Anicom Pafe Inc., Kanagawa, Japan
| | - Genki Ishihara
- Research and Development Section, Anicom Specialty Medical Institute Inc., Kanagawa, Japan
| | - Yuki Matsumoto
- Genetic Testing Section, Anicom Pafe Inc., Kanagawa, Japan
- Research and Development Section, Anicom Specialty Medical Institute Inc., Kanagawa, Japan
- Data Science Center, Azabu University, Kanagawa, Japan
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25
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Fallahi M, Masoudi AA, Torshizi RV. Genetic variants in the TAC1 transcriptional regulatory region affect on trainability and excitability levels in Belgian Malinois dogs. Vet Med Sci 2024; 10:e1346. [PMID: 38227710 PMCID: PMC10790320 DOI: 10.1002/vms3.1346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Revised: 11/12/2023] [Accepted: 12/10/2023] [Indexed: 01/18/2024] Open
Abstract
BACKGROUND Trainability in dogs is affected by learning aptitude and memory capacity. While this trait has a heritable basis in canines, the specific genetic loci responsible for it remain unknown. Our previous results suggested that the BDNF, CCK and TAC1 genes are associated with learning and memory in canines. Experimental validation is crucial to confirm the effects of these candidate genes on trainability. Understanding the genetic foundation of this trait would offer insight into the inheritance pattern of complex behavioural characteristics. OBJECTIVE This study aimed to assess the genetic variations within candidate genes and explore their potential associations with behavioural phenotypes in dogs. METHODS The behavioural characteristics of 123 male Belgian Malinois dogs were assessed using a customised questionnaire. Target regions of candidate genes were screened for genetic variation by single-strand conformational polymorphism (SSCP). Following that, SSCP banding patterns were sequenced, and putative transcription factor binding sites were predicted using bioinformatics tools. Quantitative association analysis between identified genetic variants and behavioural trait scores was performed using the general linear model (GLM). RESULTS Sequencing the coding and flanking regions revealed three mutations (c.-89C>T, c.-162G>C and c.*33T>A) in the dog TAC1 gene. Bioinformatics analysis predicted two single nucleotide polymorphisms (SNPs) were located within the putative TAC1 promoter and could disrupt transcription factor binding sites. Statistical tests revealed that the c.-89C>T was significantly associated with excitability (p < 0.01), while the c.-162G>C was significantly associated with trainability level (p < 0.05). CONCLUSION In summary, we identified two regulatory SNPs in the 5'-UTR promoter region of the TAC1 gene that are associated with excitability and trainability in Belgian Malinois dogs. These genetic variations have the potential to alter the binding sites of transcription factors NRF1 and OTX1, consequently influencing TAC1 expression and related behavioural characteristics. Our findings implicate TAC1 polymorphisms as candidates influencing breed-specific behavioural characteristics in canines. Further studies on diverse breeds of dogs are necessary to validate these SNPs' effects.
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Affiliation(s)
- Mohammad Fallahi
- Faculty of AgricultureDepartment of Animal ScienceTarbiat Modares UniversityTehranIran
| | - Ali Akbar Masoudi
- Faculty of AgricultureDepartment of Animal ScienceTarbiat Modares UniversityTehranIran
| | - Rasoul Vaez Torshizi
- Faculty of AgricultureDepartment of Animal ScienceTarbiat Modares UniversityTehranIran
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26
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Zhou BW, Wu QQ, Mauki DH, Wang X, Zhang SR, Yin TT, Chen FL, Li C, Liu YH, Wang GD, Zhang YP. Germline gene fusions across species reveal the chromosomal instability regions and cancer susceptibility. iScience 2023; 26:108431. [PMID: 38205119 PMCID: PMC10777377 DOI: 10.1016/j.isci.2023.108431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 06/24/2023] [Accepted: 11/08/2023] [Indexed: 01/12/2024] Open
Abstract
The canine transmissible venereal tumor (CTVT) is a clonal cell-mediated cancer with a long evolutionary history and extensive karyotype rearrangements in its genome. However, little is known about its genetic similarity to human tumors. Here, using multi-omics data we identified 11 germline gene fusions (GGFs) in CTVT, which showed higher genetic susceptibility than others. Additionally, we illustrate a mechanism of a complex gene fusion of three gene segments (HSD17B4-DMXL1-TNFAIP8) that we refer to "greedy fusion". Our findings also provided evidence that expressions of GGFs are downregulated during the tumor regressive phase, which is associated with DNA methylation level. This study presents a comprehensive landscape of gene fusions (GFs) in CTVT, which offers a valuable genetic resource for exploring potential genetic mechanisms underlying the development of cancers in both dogs and humans.
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Affiliation(s)
- Bo-Wen Zhou
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650204, China
| | - Qing-Qin Wu
- School of Ecology and Environmental Sciences, Yunnan University, Kunming, Yunnan 650500, China
| | - David H. Mauki
- Institute of Neurological Disease, National-Local Joint Engineering Research Center of Translational Medicine, State Key Lab of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Xuan Wang
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650204, China
| | - Shu-Run Zhang
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Ting-Ting Yin
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Fang-Liang Chen
- Kunming Police Dog Base of the Ministry of Public Security, Kunming, Yunnan 650204, China
| | - Chao Li
- State Key Laboratory for Conservation and Utilization of Bio-Resource, Yunnan University, Kunming, Yunnan 650500, China
| | - Yan-Hu Liu
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Guo-Dong Wang
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650204, China
| | - Ya-Ping Zhang
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650204, China
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27
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Muscatello LV, Frabetti S, Avallone G, Gobbo F, Pasquini A, D'Annunzio G, Pisoni L, Marconato L, Terragni R, De Biase D, Candini O, Sarli G. Morphologic, phenotypic, and genotypic similarities between primary tumors and corresponding 3D cell cultures grown in a repeatable system-preliminary results. BMC Vet Res 2023; 19:263. [PMID: 38071286 PMCID: PMC10709889 DOI: 10.1186/s12917-023-03834-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 11/30/2023] [Indexed: 12/18/2023] Open
Abstract
BACKGROUND Three-dimensional (3D) cell cultures are the new frontier for reproducing the tumor micro-environment in vitro. The aims of the study were (1) to establish primary 3D cell cultures from canine spontaneous neoplasms and (2) to demonstrate the morphological, phenotypic and genotypic similarities between the primary canine neoplasms and the corresponding 3D cultures, through the expression of tumor differentiation markers. RESULTS Seven primary tumors were collected, including 4 carcinomas and 3 soft tissue sarcomas. 3D cell cultures reproduced the morphological features of the primary tumors and showed an overlapping immunophenotype of the primary epithelial tumors. Immunohistochemistry demonstrated the growth of stromal cells and macrophages admixed with the neoplastic epithelial component, reproducing the tumor microenvironment. Mesenchymal 3D cultures reproduced the immunophenotype of the primary tumor completely in 2 out of 3 examined cases while a discordant expression was documented for a single marker in one case. No single nucleotide variants or small indel were detected in TP53 or MDM2 genes, both in primary tumors and in 3D cell cultures specimens. In one sample, MDM2 amplicons were preferentially increased in number compared to TP53 ones, indicating amplification of MDM2, detectable both in the primary tumor and in the corresponding cell culture specimen. CONCLUSION Here we demonstrate a good cell morphology, phenotype and genetic profile overlap between primary tumors and the corresponding 3D cultures grown in a repeatable system.
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Affiliation(s)
- Luisa Vera Muscatello
- Department of Veterinary Medical Sciences, University of Bologna, I-40064, Ozzano dell'Emilia, BO, Italy.
| | | | - Giancarlo Avallone
- Department of Veterinary Medical Sciences, University of Bologna, I-40064, Ozzano dell'Emilia, BO, Italy
| | - Francesca Gobbo
- Department of Veterinary Medical Sciences, University of Bologna, I-40064, Ozzano dell'Emilia, BO, Italy
| | - Arianna Pasquini
- Department of Veterinary Medical Sciences, University of Bologna, I-40064, Ozzano dell'Emilia, BO, Italy
| | - Giulia D'Annunzio
- Department of Veterinary Medical Sciences, University of Bologna, I-40064, Ozzano dell'Emilia, BO, Italy
- Experimental Zooprophylactic Institute of Lombardia and Emilia Romagna, I-25124, Brescia, Italy
| | - Luciano Pisoni
- Department of Veterinary Medical Sciences, University of Bologna, I-40064, Ozzano dell'Emilia, BO, Italy
| | - Laura Marconato
- Department of Veterinary Medical Sciences, University of Bologna, I-40064, Ozzano dell'Emilia, BO, Italy
| | | | - Dario De Biase
- Department of Pharmacy and BiotechnologyUniversity of Bologna, I-40127, Bologna, Italy
| | | | - Giuseppe Sarli
- Department of Veterinary Medical Sciences, University of Bologna, I-40064, Ozzano dell'Emilia, BO, Italy
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Heishima K, Aketa N, Heishima M, Kawachi A. Hemangiosarcoma in dogs as a potential non-rodent animal model for drug discovery research of angiosarcoma in humans. Front Oncol 2023; 13:1250766. [PMID: 38130992 PMCID: PMC10733437 DOI: 10.3389/fonc.2023.1250766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 11/06/2023] [Indexed: 12/23/2023] Open
Abstract
Since the domestication of dogs 10,000 years ago, they have shared their living environment with humans and have co-evolved. The breeding process that dogs have undergone in only a few centuries has led to a significant accumulation of specific genetic alterations that could induce particular diseases in certain breeds. These canine diseases are similar to what is found in humans with several differences; therefore, comparing such diseases occurring in humans and dogs can help discover novel disease mechanisms, pathways, and causal genetic factors. Human angiosarcoma (AS) and canine hemangiosarcoma (HSA), which are sarcomas originating from endothelium, are examples of diseases shared between humans and dogs. They exhibit similar characteristics and clinical behaviors, although with some critical differences resulting from evolution. In this review, we will describe the similarities and differences in terms of clinical and molecular characteristics between human AS and canine HSA, and discuss how these similarities and differences can be applied to advance the treatment of these diseases.
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Affiliation(s)
- Kazuki Heishima
- Institute for Advanced Study (GUiAS), Gifu University, Gifu, Japan
- Center for One Medicine Innovative Translational Research (COMIT), Gifu University, Gifu, Japan
| | - Naohiko Aketa
- Clinical and Translational Research Center, Keio University Hospital, Tokyo, Japan
| | | | - Asuka Kawachi
- Division of Cancer RNA Research, National Cancer Center, Tokyo, Japan
- Department of Medical Oncology, National Cancer Center Hospital, Tokyo, Japan
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29
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Benítez-Burraco A, Uriagereka J, Nataf S. The genomic landscape of mammal domestication might be orchestrated by selected transcription factors regulating brain and craniofacial development. Dev Genes Evol 2023; 233:123-135. [PMID: 37552321 PMCID: PMC10746608 DOI: 10.1007/s00427-023-00709-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Accepted: 07/27/2023] [Indexed: 08/09/2023]
Abstract
Domestication transforms once wild animals into tamed animals that can be then exploited by humans. The process entails modifications in the body, cognition, and behavior that are essentially driven by differences in gene expression patterns. Although genetic and epigenetic mechanisms were shown to underlie such differences, less is known about the role exerted by trans-regulatory molecules, notably transcription factors (TFs) in domestication. In this paper, we conducted extensive in silico analyses aimed to clarify the TF landscape of mammal domestication. We first searched the literature, so as to establish a large list of genes selected with domestication in mammals. From this list, we selected genes experimentally demonstrated to exhibit TF functions. We also considered TFs displaying a statistically significant number of targets among the entire list of (domestication) selected genes. This workflow allowed us to identify 5 candidate TFs (SOX2, KLF4, MITF, NR3C1, NR3C2) that were further assessed in terms of biochemical and functional properties. We found that such TFs-of-interest related to mammal domestication are all significantly involved in the development of the brain and the craniofacial region, as well as the immune response and lipid metabolism. A ranking strategy, essentially based on a survey of protein-protein interactions datasets, allowed us to identify SOX2 as the main candidate TF involved in domestication-associated evolutionary changes. These findings should help to clarify the molecular mechanics of domestication and are of interest for future studies aimed to understand the behavioral and cognitive changes associated to domestication.
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Affiliation(s)
- Antonio Benítez-Burraco
- Department of Spanish, Linguistics, and Theory of Literature (Linguistics), Faculty of Philology, University of Seville, Seville, Spain.
- Área de Lingüística General, Departamento de Lengua Española, Lingüística y Teoría de la Literatura, Facultad de Filología, Universidad de Sevilla, C/ Palos de la Frontera s/n., 41007-, Sevilla, España.
| | - Juan Uriagereka
- Department of Linguistics and School of Languages, Literatures & Cultures, University of Maryland, College Park, MD, USA
| | - Serge Nataf
- Stem-cell and Brain Research Institute, 18 avenue de Doyen Lépine, F-69500, Bron, France
- University of Lyon 1, 43 Bd du 11 Novembre 1918, F-69100, Villeurbanne, France
- Bank of Tissues and Cells, Hospices Civils de Lyon, Hôpital Edouard Herriot, Place d'Arsonval, F-69003, Lyon, France
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30
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Konno A, Aoki H, Suzuki E, Furuta S, Ueda S. Are dark-eyed dogs favoured by humans? Domestication as a potential driver of iris colour difference between dogs and wolves. ROYAL SOCIETY OPEN SCIENCE 2023; 10:230854. [PMID: 38126061 PMCID: PMC10731317 DOI: 10.1098/rsos.230854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 11/27/2023] [Indexed: 12/23/2023]
Abstract
Comparative studies have shown that the eye morphology of primates has been shaped by a variety of selection pressures (e.g. communication, environmental factors). To comprehensively elucidate the complex links between ocular morphology and its evolutionary drive, attention should be paid to other phylogenetic groups. Here, we address a new question regarding the evolution of eye colour patterns in the oldest domesticated animal, namely, the domestic dog (Canis familiaris). In this study, we conducted an image analysis of dogs and their closest relatives, grey wolves (Canis lupus), to compare the colours of their irises, with the aim of assessing whether eye colours of dogs affect how humans perceived dogs. We found that the irises of dogs were significantly darker than those of wolves. We also found that facial images of dark-eyed dogs were perceived as more friendly and immature, potentially eliciting caregiving responses from humans. Our findings are consistent with our expectation that humans favour dark-eyed dogs over light-eyed ones and provide an updated hypothesis that dogs with dark eyes may have evolved by acquiring a facial trait that sends a non-threatening gaze signal to humans.
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Affiliation(s)
- Akitsugu Konno
- Department of Animal Sciences, Teikyo University of Science, Yamanashi, Japan
| | - Hitomi Aoki
- Department of Animal Sciences, Teikyo University of Science, Yamanashi, Japan
| | - Emiri Suzuki
- Department of Animal Sciences, Teikyo University of Science, Yamanashi, Japan
| | - Seiya Furuta
- Department of Animal Sciences, Teikyo University of Science, Yamanashi, Japan
| | - Sayoko Ueda
- The Mt. Fuji Institute for Nature and Biology, Showa University, Yamanashi, Japan
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31
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Kyriazis CC, Robinson JA, Lohmueller KE. Using Computational Simulations to Model Deleterious Variation and Genetic Load in Natural Populations. Am Nat 2023; 202:737-752. [PMID: 38033186 PMCID: PMC10897732 DOI: 10.1086/726736] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2023]
Abstract
AbstractDeleterious genetic variation is abundant in wild populations, and understanding the ecological and conservation implications of such variation is an area of active research. Genomic methods are increasingly used to quantify the impacts of deleterious variation in natural populations; however, these approaches remain limited by an inability to accurately predict the selective and dominance effects of mutations. Computational simulations of deleterious variation offer a complementary tool that can help overcome these limitations, although such approaches have yet to be widely employed. In this perspective article, we aim to encourage ecological and conservation genomics researchers to adopt greater use of computational simulations to aid in deepening our understanding of deleterious variation in natural populations. We first provide an overview of the components of a simulation of deleterious variation, describing the key parameters involved in such models. Next, we discuss several approaches for validating simulation models. Finally, we compare and validate several recently proposed deleterious mutation models, demonstrating that models based on estimates of selection parameters from experimental systems are biased toward highly deleterious mutations. We describe a new model that is supported by multiple orthogonal lines of evidence and provide example scripts for implementing this model (https://github.com/ckyriazis/simulations_review).
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32
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Mujica PC, Martinez V. A purebred South American breed showing high effective population size and independent breed ancestry: The Chilean Terrier. Anim Genet 2023; 54:772-785. [PMID: 37778752 DOI: 10.1111/age.13359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 08/31/2023] [Accepted: 09/09/2023] [Indexed: 10/03/2023]
Abstract
The Chilean Terrier is a known breed in Chile that has not been genetically assessed despite its distinctive color patterns, agility, and hardiness across the diversity of climates encountered within the Chilean landscape. The population structure and its relatedness with other breeds, as well as the actual origin of the breed, remain unknown. We estimated several population parameters using samples from individuals representing the distribution of the Chilean Terrier across the country. By utilizing the Illumina HD canine genotyping array, we computed the effective population size (Ne ), individual inbreeding, and relatedness to evaluate the genetic diversity of the breed. The results show that linkage disequilibrium was relatively low and decayed rapidly; in fact, Ne was very high when compared to other breeds, and similar to other American indigenous breeds (such as the Chihuahua with values of Ne near 500). These results are in line with the low estimates of genomic inbreeding and relatedness and the relatively large number of effective chromosome segments (Me = 2467) obtained using the properties of the genomic relationship matrix. Between population analysis (cross-population extended haplotype homozygosity, di ) with other breeds such as the Jack Russell Terrier, the Peruvian-Inca Orchid, and the Chihuahua suggested that candidate regions harboring FGF5, PAX3, and ASIP, probably explained some morphological traits, such as the distinctive color pattern characteristic of the breed. When considering Admixture estimates and phylogenetic analysis, together with other breeds of American and European origin, the Chilean Terrier does not have a recent European ancestry. Overall, the results suggest that the breed has evolved independently in Chile from other terrier breeds, from an unknown European terrier ancestor.
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Affiliation(s)
- Paola C Mujica
- FAVET-INBIOGEN Laboratory, Faculty of Veterinary Sciences, Universidad de Chile, Santiago, Chile
| | - Víctor Martinez
- FAVET-INBIOGEN Laboratory, Faculty of Veterinary Sciences, Universidad de Chile, Santiago, Chile
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33
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Fernandes AP, OhAinle M, Esteves PJ. Patterns of Evolution of TRIM Genes Highlight the Evolutionary Plasticity of Antiviral Effectors in Mammals. Genome Biol Evol 2023; 15:evad209. [PMID: 37988574 PMCID: PMC10709114 DOI: 10.1093/gbe/evad209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 11/03/2023] [Accepted: 11/07/2023] [Indexed: 11/23/2023] Open
Abstract
The innate immune system of mammals is formed by a complex web of interacting proteins, which together constitute the first barrier of entry for infectious pathogens. Genes from the E3-ubiquitin ligase tripartite motif (TRIM) family have been shown to play an important role in the innate immune system by restricting the activity of different retrovirus species. For example, TRIM5 and TRIM22 have both been associated with HIV restriction and are regarded as crucial parts of the antiretroviral machinery of mammals. Our analyses of positive selection corroborate the great significance of these genes for some groups of mammals. However, we also show that many species lack TRIM5 and TRIM22 altogether. By analyzing a large number of mammalian genomes, here we provide the first comprehensive view of the evolution of these genes in eutherians, showcasing that the pattern of accumulation of TRIM genes has been dissimilar across mammalian orders. Our data suggest that these differences are caused by the evolutionary plasticity of the immune system of eutherians, which have adapted to use different strategies to combat retrovirus infections. Altogether, our results provide insights into the dissimilar evolution of a representative family of restriction factors, highlighting an example of adaptive and idiosyncratic evolution in the innate immune system.
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Affiliation(s)
- Alexandre P Fernandes
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal
| | - Molly OhAinle
- Division of Immunology and Molecular Medicine, Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, California, USA
| | - Pedro J Esteves
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal
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34
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Jarosz AS, Pendleton AL, Lashbrook MJ, Cech E, Altieri M, Kunch A, Modiano JF, Halo JV. Expression and high levels of insertional polymorphism of an endogenous gammaretrovirus lineage in dogs. PLoS Genet 2023; 19:e1011083. [PMID: 38055724 PMCID: PMC10727363 DOI: 10.1371/journal.pgen.1011083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 12/18/2023] [Accepted: 11/22/2023] [Indexed: 12/08/2023] Open
Abstract
Despite the absence of a confirmed exogenously replicating retrovirus in Canis lupus familiaris (C. familiaris), past retroviral infections are evident in the genomes of living animals via the presence of endogenous retroviruses (ERVs). Although gammaretrovirus-like transcripts and enzyme activities were previously reported to be present in canine leukemias and lymphomas, those findings were not further explored. Initial analysis of the C. familiaris reference genome revealed a minor subset of one ERV lineage, classified as CfERV-Fc1(a), or Fc1(a) here, with features characteristic of recent integration, including the presence of ORFs and identical or nearly identical LTRs. Our previous analysis of whole genome sequence data belonging to extant Canidae revealed a burst of past infections in Canis ancestors resulting in numerous young, polymorphic, and highly intact loci now segregating in dogs. Here, we demonstrate the expression of full-length Fc1(a) proviruses in tissues collected from healthy animals and from animals with cancer. We observed significantly higher expression in samples of dogs with various cancer diagnoses when compared to samples from healthy dogs. Genotyping of insertionally polymorphic Fc1(a) loci identified candidate expressed proviruses and delineated distributions over sample groups. Collectively, the data show that Fc1(a) proviruses retain biological activity in the domestic dog and provides a means to examine potential genetic links with disease states in this species.
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Affiliation(s)
- Abigail S. Jarosz
- Bowling Green State University, Department of Biological Sciences, Bowling Green, Ohio, United States of America
| | - Amanda L. Pendleton
- Purdue University, Department of Biochemistry, West Lafayette, Indiana, United States of America
- Purdue University, Purdue Center for Plant Biology, West Lafayette, Indiana, United States of America
| | - Michael J. Lashbrook
- Bowling Green State University, Department of Biological Sciences, Bowling Green, Ohio, United States of America
| | - Erica Cech
- Bowling Green State University, Department of Biological Sciences, Bowling Green, Ohio, United States of America
| | - Madison Altieri
- Bowling Green State University, Department of Biological Sciences, Bowling Green, Ohio, United States of America
| | - Austin Kunch
- Bowling Green State University, Department of Biological Sciences, Bowling Green, Ohio, United States of America
| | - Jaime F. Modiano
- Animal Cancer Care and Research Program, University of Minnesota, St. Paul, Minnesota, United States of America
- Department of Veterinary Clinical Sciences, College of Veterinary Medicine, University of Minnesota, St. Paul, Minnesota, United States of America
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, United States of America
- Center for Immunology, University of Minnesota, Minneapolis, Minnesota, United States of America
- Stem Cell Institute, University of Minnesota, Minneapolis, Minnesota, United States of America
- Institute for Engineering in Medicine, University of Minnesota, Minneapolis, Minnesota, United States of America
- Department of Laboratory Medicine and Pathology, Medical School, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Julia V. Halo
- Bowling Green State University, Department of Biological Sciences, Bowling Green, Ohio, United States of America
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35
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Cocostîrc V, Paștiu AI, Pusta DL. An Overview of Canine Inherited Neurological Disorders with Known Causal Variants. Animals (Basel) 2023; 13:3568. [PMID: 38003185 PMCID: PMC10668755 DOI: 10.3390/ani13223568] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 11/15/2023] [Accepted: 11/15/2023] [Indexed: 11/26/2023] Open
Abstract
Hereditary neurological conditions documented in dogs encompass congenital, neonatal, and late-onset disorders, along with both progressive and non-progressive forms. In order to identify the causal variant of a disease, the main two approaches are genome-wide investigations and candidate gene investigation. Online Mendelian Inheritance in Animals currently lists 418 Mendelian disorders specific to dogs, of which 355 have their likely causal genetic variant identified. This review aims to summarize the current knowledge on the canine nervous system phenes and their genetic causal variant. It has been noted that the majority of these diseases have an autosomal recessive pattern of inheritance. Additionally, the dog breeds that are more prone to develop such diseases are the Golden Retriever, in which six inherited neurological disorders with a known causal variant have been documented, and the Belgian Shepherd, in which five such disorders have been documented. DNA tests can play a vital role in effectively managing and ultimately eradicating inherited diseases.
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Affiliation(s)
- Vlad Cocostîrc
- Department of Genetics and Hereditary Diseases, Faculty of Veterinary Medicine, University of Agricultural Sciences and Veterinary Medicine Cluj-Napoca, 400372 Cluj-Napoca, Romania; (A.I.P.); (D.L.P.)
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36
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Sacco JC, Starr E, Weaver A, Dietz R, Spocter MA. Resequencing of the TMF-1 (TATA Element Modulatory Factor) regulated protein (TRNP1) gene in domestic and wild canids. Canine Med Genet 2023; 10:10. [PMID: 37968761 PMCID: PMC10647097 DOI: 10.1186/s40575-023-00133-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 10/27/2023] [Indexed: 11/17/2023] Open
Abstract
BACKGROUND Cortical folding is related to the functional organization of the brain. The TMF-1 regulated protein (TRNP1) regulates the expansion and folding of the mammalian cerebral cortex, a process that may have been accelerated by the domestication of dogs. The objectives of this study were to sequence the TRNP1 gene in dogs and related canid species, provide evidence of its expression in dog brain and compare the genetic variation within dogs and across the Canidae. The gene was located in silico to dog chromosome 2. The sequence was experimentally confirmed by amplifying and sequencing the TRNP1 exonic and promoter regions in 72 canids (36 purebred dogs, 20 Gy wolves and wolf-dog hybrids, 10 coyotes, 5 red foxes and 1 Gy fox). RESULTS A partial TRNP1 transcript was isolated from several regions in the dog brain. Thirty genetic polymorphisms were found in the Canis sp. with 17 common to both dogs and wolves, and only one unique to dogs. Seven polymorphisms were observed only in coyotes. An additional 9 variants were seen in red foxes. Dogs were the least genetically diverse. Several polymorphisms in the promoter and 3'untranslated region were predicted to alter TRNP1 function by interfering with the binding of transcriptional repressors and miRNAs expressed in neural precursors. A c.259_264 deletion variant that encodes a polyalanine expansion was polymorphic in all species studied except for dogs. A stretch of 15 nucleotides that is found in other mammalian sequences (corresponding to 5 amino acids located between Pro58 and Ala59 in the putative dog protein) was absent from the TRNP1 sequences of all 5 canid species sequenced. Both of these aforementioned coding sequence variations were predicted to affect the formation of alpha helices in the disordered region of the TRNP1 protein. CONCLUSIONS Potentially functionally important polymorphisms in the TRNP1 gene are found within and across various Canis species as well as the red fox, and unique differences in protein structure have evolved and been conserved in the Canidae compared to all other mammalian species.
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Affiliation(s)
- James C Sacco
- Ellis Pharmacogenomics Laboratory, College of Pharmacy and Health Sciences, Drake University, 50311, Des Moines, IA, USA.
| | - Emma Starr
- Ellis Pharmacogenomics Laboratory, College of Pharmacy and Health Sciences, Drake University, 50311, Des Moines, IA, USA
| | - Alyssa Weaver
- Ellis Pharmacogenomics Laboratory, College of Pharmacy and Health Sciences, Drake University, 50311, Des Moines, IA, USA
| | - Rachel Dietz
- Ellis Pharmacogenomics Laboratory, College of Pharmacy and Health Sciences, Drake University, 50311, Des Moines, IA, USA
| | - Muhammad A Spocter
- Department of Anatomy, Des Moines University, 50266, Des Moines, IA, USA
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Senhorello ILS, Matiz ORS, Canavari IC, Hernandez GV, Anai LA, Navarrete Ampuero RA, Pazzini JM, Prado CM, Meirelles FV, Vasconcelos RDO, Tinucci-Costa EM. Expression of acetylated histones H3 and H4 and histone deacetylase enzymes HDAC1, HDAC2 and HDAC6 in simple mammary carcinomas of female dogs. Front Genet 2023; 14:1257932. [PMID: 38028583 PMCID: PMC10666162 DOI: 10.3389/fgene.2023.1257932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 10/05/2023] [Indexed: 12/01/2023] Open
Abstract
Histone deacetylation is an important mechanism involved in human breast cancer tumorigenesis and recent veterinary oncology studies also demonstrate a similar relationship in some canine neoplasms. The use of HDAC inhibitors in vitro and in vivo has demonstrated antitumor action on several strains of human and animal cancers. The present study aims to correlate the expression of H3K9Ac, H4K12Ac, HDAC1, HDAC2 and HDAC6 in simple mammary carcinomas in dogs with clinicopathological parameters and overall survival time. To this end, 61 samples of simple breast carcinomas were analyzed by the immunohistochemistry technique with subsequent validation of the antibodies by the Western Blot technique. The expressions obtained via a semi-quantitative way were categorized by assigning scores and classified into high or low expressions according to the given score, except for HDAC6, when the marking percentage was considered and subdivided into high and low expressions using the median value. For statistical analysis, the chi-square test or Fisher exact test were used as univariate analysis and correspondence analysis as a multivariate test, in addition to the Kaplan-Meier survival analysis. In the studied samples, the highest frequencies were determined for the high expression proteins H4K12Ac (88.5%), HDAC2 (65.6%) and HDAC6 (56.7%) and the low expression proteins H3K9Ac (73.8%) and HDAC1 (54.1%). An association between the low expression of HDAC1 and the presence of lymph node metastasis (p = 0.035) was indicated by univariate analysis while the high expression of HDAC1 was associated with favorable prognostic factors, such as the absence of lymph node metastasis and low mitotic index by multivariate analysis. Also, by multivariate analysis, the low expression of HDAC6 was correlated with the low expression of Ki67, smaller tumors, and better prognosis factors as well. Protein expression was not correlated with patients' overall survival time (p > 0.05). The high expressions of HDAC2 and HDAC6 in mammary carcinomas in female dogs may be useful information for research involving therapeutic targets with iHDACs since their inhibition favors hyperacetylation and transcription of tumor suppressor genes.
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Affiliation(s)
- Igor Luiz Salardani Senhorello
- Department of Veterinary Clinic and Surgery, Faculty of Agricultural and Veterinary Sciences, Universidade Estadual Paulista, Jaboticabal, SP, Brazil
- Department of Veterinarry Medicine, Universidade Vila Velha-UVV, Vila Velha, Espírito Santo, Brazil
| | - Oscar Rodrigo Sierra Matiz
- Department of Veterinary Clinic and Surgery, Faculty of Agricultural and Veterinary Sciences, Universidade Estadual Paulista, Jaboticabal, SP, Brazil
| | - Isabela Cristina Canavari
- Department of Veterinary Clinic and Surgery, Faculty of Agricultural and Veterinary Sciences, Universidade Estadual Paulista, Jaboticabal, SP, Brazil
| | | | | | | | | | - Cibele Maria Prado
- Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering, Universidade de São Paulo-USP, Pirassununga, São Paulo, Brazil
| | - Flavio Vieira Meirelles
- Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering, Universidade de São Paulo-USP, Pirassununga, São Paulo, Brazil
| | - Rosemeri de Oliveira Vasconcelos
- Department of Veterinary Clinic and Surgery, Faculty of Agricultural and Veterinary Sciences, Universidade Estadual Paulista, Jaboticabal, SP, Brazil
| | - e Mirela Tinucci-Costa
- Department of Veterinary Clinic and Surgery, Faculty of Agricultural and Veterinary Sciences, Universidade Estadual Paulista, Jaboticabal, SP, Brazil
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Lyu Q, Veldhuizen EJA, Ludwig IS, Rutten VPMG, van Eden W, Sijts AJAM, Broere F. Characterization of polarization states of canine monocyte derived macrophages. PLoS One 2023; 18:e0292757. [PMID: 37939066 PMCID: PMC10631683 DOI: 10.1371/journal.pone.0292757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Accepted: 09/27/2023] [Indexed: 11/10/2023] Open
Abstract
Macrophages can reversibly polarize into multiple functional subsets depending on their micro-environment. Identification and understanding the functionality of these subsets is relevant for the study of immune‑related diseases. However, knowledge about canine macrophage polarization is still in its infancy. In this study, we polarized canine monocytes using GM-CSF/IFN- γ and LPS towards M1 macrophages or M-CSF and IL-4 towards M2 macrophages and compared them to undifferentiated monocytes (M0). Polarized M1 and M2 macrophages were thoroughly characterized for morphology, surface marker features, gene profiles and functional properties. Our results showed that canine M1-polarized macrophages obtained a characteristic large, roundish, or amoeboid shape, while M2-polarized macrophages were smaller and adopted an elongated spindle-like morphology. Phenotypically, all macrophage subsets expressed the pan-macrophage markers CD14 and CD11b. M1-polarized macrophages expressed increased levels of CD40, CD80 CD86 and MHC II, while a significant increase in the expression levels of CD206, CD209, and CD163 was observed in M2-polarized macrophages. RNAseq of the three macrophage subsets showed distinct gene expression profiles, which are closely associated with immune responsiveness, cell differentiation and phagocytosis. However, the complexity of the gene expression patterns makes it difficult to assign clear new polarization markers. Functionally, undifferentiated -monocytes, and M1- and M2- like subsets of canine macrophages can all phagocytose latex beads. M2-polarized macrophages exhibited the strongest phagocytic capacity compared to undifferentiated monocytes- and M1-polarized cells. Taken together, this study showed that canine M1 and M2-like macrophages have distinct features largely in parallel to those of well-studied species, such as human, mouse and pig. These findings enable future use of monocyte derived polarized macrophages particularly in studies of immune related diseases in dogs.
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Affiliation(s)
- Qingkang Lyu
- Department Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
- Immunology Center of Georgia, Augusta University, Augusta, GA, United States of America
| | - Edwin J. A. Veldhuizen
- Department Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Irene S. Ludwig
- Department Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Victor P. M. G. Rutten
- Department Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
- Department of Veterinary Tropical diseases, Faculty of Veterinary Science, Pretoria University, Pretoria, South Africa
| | - Willem van Eden
- Department Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Alice J. A. M. Sijts
- Department Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Femke Broere
- Department Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
- Department of Clinical Sciences of Companion Animals, Faculty Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
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Bannasch DL, Oertle DT, Vo J, Batcher KL, Stern JA, Kaplan JL, Li RHL, Madden IE, Christen M, Leeb T, Joshi N. Naturally occurring canine laminopathy leading to a dilated and fibrosing cardiomyopathy in the Nova Scotia Duck Tolling Retriever. Sci Rep 2023; 13:19077. [PMID: 37925523 PMCID: PMC10625583 DOI: 10.1038/s41598-023-46601-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 11/02/2023] [Indexed: 11/06/2023] Open
Abstract
Dilated cardiomyopathy (DCM) is characterized by decreased systolic function and dilation of one or both ventricles, often leading to heart failure or sudden death. Two 10-month-old sibling Nova Scotia Duck Tolling Retrievers (NSDTR) died acutely with evidence of dilated cardiomyopathy with myocardial fibrosis. Association analysis using two cases and 35 controls identified three candidate regions homozygous in the two cases. Whole genome sequencing identified a frameshift deletion in the LMNA gene (NC_049228.1:g.41688530del, NP_001274080:p.(Asp576ThrfsTer124)). Three retrospectively identified NSDTRs with sudden death before 2 years of age and severe myocardial fibrosis were also homozygous for the deletion. One 5 year old with sudden death and myocardial fibrosis was heterozygous for the deletion. This variant was not identified in 722 dogs of other breeds, nor was it identified to be homozygous in 784 NSDTR. LMNA codes for lamin A/C proteins, which are type V intermediate filaments that provide structural support to the nuclear membrane. In humans, LMNA variants can cause DCM with sudden death as well as diseases of striated muscles, lipodystrophy, neuropathies, and accelerated aging disorders. This frameshift deletion is predicted to affect processing of prelamin A into lamin A. Pedigree analysis in the NSDTR and functional evaluation of heterozygotes is consistent with a predominantly recessive mode of inheritance and possibly low penetrance in heterozygotes in contrast to people, where most pathogenic LMNA variants are dominantly inherited.
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Affiliation(s)
- Danika L Bannasch
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California Davis, Davis, CA, USA.
| | - Danielle T Oertle
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California Davis, Davis, CA, USA
| | - Julia Vo
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California Davis, Davis, CA, USA
| | - Kevin L Batcher
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California Davis, Davis, CA, USA
| | - Joshua A Stern
- Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California Davis, Davis, CA, USA
| | - Joanna L Kaplan
- Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California Davis, Davis, CA, USA
| | - Ronald H L Li
- Department of Surgical and Radiological Sciences, School of Veterinary Medicine, University of California Davis, Davis, CA, USA
| | - Indiana E Madden
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California Davis, Davis, CA, USA
| | - Matthias Christen
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001, Bern, Switzerland
| | - Tosso Leeb
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001, Bern, Switzerland
| | - Nikhil Joshi
- Bioinformatics Core, UC Davis Genome Center, University of California, Davis, CA, USA
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Schall PZ, Winkler PA, Petersen-Jones SM, Yuzbasiyan-Gurkan V, Kidd JM. Genome-wide methylation patterns from canine nanopore assemblies. G3 (BETHESDA, MD.) 2023; 13:jkad203. [PMID: 37681359 PMCID: PMC10627269 DOI: 10.1093/g3journal/jkad203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 08/23/2023] [Accepted: 08/29/2023] [Indexed: 09/09/2023]
Abstract
Recent advances in long-read sequencing have enabled the creation of reference-quality genome assemblies for multiple individuals within a species. In particular, 8 long-read genome assemblies have recently been published for the canine model (dogs and wolves). These assemblies were created using a range of sequencing and computational approaches, with only limited comparisons described among subsets of the assemblies. Here we present 3 high-quality de novo reference assemblies based upon Oxford Nanopore long-read sequencing: 2 Bernese Mountain Dogs (BD & OD) and a Cairn terrier (CA611). These breeds are of particular interest due to the enrichment of unresolved genetic disorders. Leveraging advancement in software technologies, we utilized published data of Labrador Retriever (Yella) to generate a new assembly, resulting in a ∼280-fold increase in continuity (N50 size of 91 kbp vs 25.75 Mbp). In conjunction with these 4 new assemblies, we uniformly assessed 8 existing assemblies for generalized quality metrics, sequence divergence, and a detailed BUSCO assessment. We identified a set of ∼400 conserved genes during the BUSCO analysis missing in all assemblies. Genome-wide methylation profiles were generated from the nanopore sequencing, resulting in broad concordance with existing whole-genome and reduced-representation bisulfite sequencing, while highlighting superior overage of mobile elements. These analyses demonstrate the ability of Nanopore sequencing to resolve the sequence and epigenetic profile of canine genomes.
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Affiliation(s)
- Peter Z Schall
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Paige A Winkler
- Department of Small Animal Clinical Sciences, College of Veterinary Medicine, Michigan State University, East Lansing, MI 48824, USA
| | - Simon M Petersen-Jones
- Department of Small Animal Clinical Sciences, College of Veterinary Medicine, Michigan State University, East Lansing, MI 48824, USA
| | - Vilma Yuzbasiyan-Gurkan
- Department of Small Animal Clinical Sciences, College of Veterinary Medicine, Michigan State University, East Lansing, MI 48824, USA
- Department of Microbiology and Molecular Genetics, College of Veterinary Medicine, Michigan State University, East Lansing, MI 48824, USA
| | - Jeffrey M Kidd
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
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41
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Ke C, Sio K, Wu C, Xia Y, Lee J, Hu C, Liu C, Lu C, Cheng C, Lin K, Tomiyasu H, Wang Y, Lin C. Increased plasma DR-70 (fibrinogen-fibrin degradation products) concentrations as a diagnostic biomarker in dogs with neoplasms. J Vet Intern Med 2023; 37:2391-2401. [PMID: 37837297 PMCID: PMC10658483 DOI: 10.1111/jvim.16898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 09/27/2023] [Indexed: 10/15/2023] Open
Abstract
BACKGROUND Tumor biomarkers have used widely in clinical oncology in human medicine. Only a few studies have evaluated the clinical utility of tumor biomarkers for veterinary medicine. A test for fibrinogen and fibrin degradation products (DR-70) has been proposed as an ideal biomarker for tumors in humans. The clinical value of DR-70 for veterinary medicine however has yet to be determined. OBJECTIVES Investigate the diagnostic value of DR-70 concentrations by comparing them between healthy dogs and dogs with tumors. ANIMALS Two hundred sixty-three dogs with different types of tumors were included. Sixty healthy dogs also were recruited for comparison. METHODS The DR-70 concentrations were measured in all recruited individuals by ELISA. Clinical conditions were categorized based on histopathology, cytology, ultrasound examination, radiology, clinical findings, and a combination of these tests. RESULTS The median concentration of DR-70 was 2.130 ± 0.868 μg/mL in dogs with tumors, which was significantly higher than in healthy dogs (1.202 ± 0.610 μg/mL; P < .0001). With a cut-off of 1.514 μg/mL, the sensitivity and specificity of DR-70 were 84.03% and 78.33%, respectively. The area under curve was 0.883. The DR-70 concentration can be an effective tumor biomarker in veterinary medicine. CONCLUSIONS AND CLINICAL IMPORTANCE Increased DR-70 concentrations were not affected by tumor type, sex, age, or body weight. However, in dogs with metastatic mast cell tumors and oral malignant melanoma, DR-70 concentrations were significantly increased. Additional studies, including more dogs with nonneoplastic diseases, are needed to further evaluate the usefulness of DR-70 as a tumor biomarker.
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Affiliation(s)
- Chiao‐Hsu Ke
- Department of Veterinary Medicine, School of Veterinary MedicineNational Taiwan UniversityTaipei 10617Taiwan, ROC
| | - Ka‐Mei Sio
- Department of Veterinary Medicine, School of Veterinary MedicineNational Taiwan UniversityTaipei 10617Taiwan, ROC
| | - Chun‐Hung Wu
- Wellcarevet Animal HospitalTaipei 11460Taiwan, ROC
| | - Yuan‐Yuan Xia
- Graduate Institute of Veterinary Clinical Science, School of Veterinary MedicineNational Taiwan UniversityTaipei 10617Taiwan, ROC
- Animal Cancer Center, College of Bioresources and AgricultureNational Taiwan UniversityTaipei 10617Taiwan, ROC
- National Taiwan University Veterinary Hospital, College of Bioresources and AgricultureNational Taiwan UniversityTaipei 10672Taiwan, ROC
| | - Jih‐Jong Lee
- Graduate Institute of Veterinary Clinical Science, School of Veterinary MedicineNational Taiwan UniversityTaipei 10617Taiwan, ROC
- Animal Cancer Center, College of Bioresources and AgricultureNational Taiwan UniversityTaipei 10617Taiwan, ROC
- National Taiwan University Veterinary Hospital, College of Bioresources and AgricultureNational Taiwan UniversityTaipei 10672Taiwan, ROC
| | - Chin‐Hao Hu
- Lifecare Animal HospitalTaipei 11271Taiwan, ROC
| | - Cheng‐Chi Liu
- Department of Veterinary Medicine, School of Veterinary MedicineNational Taiwan UniversityTaipei 10617Taiwan, ROC
| | | | | | | | - Hirotaka Tomiyasu
- Department of Veterinary Medical SciencesThe University of TokyoTokyo 113‐8657Japan
| | - Yu‐Shan Wang
- Department of Veterinary Medicine, School of Veterinary MedicineNational Taiwan UniversityTaipei 10617Taiwan, ROC
- Uni‐Pharma Co‐Ltd.Taipei 11494Taiwan, ROC
| | - Chen‐Si Lin
- Department of Veterinary Medicine, School of Veterinary MedicineNational Taiwan UniversityTaipei 10617Taiwan, ROC
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Lee BT, Baker LA, Momen M, Terhaar H, Binversie EE, Sample SJ, Muir P. Identification of genetic variants associated with anterior cruciate ligament rupture and AKC standard coat color in the Labrador Retriever. BMC Genom Data 2023; 24:60. [PMID: 37884875 PMCID: PMC10605342 DOI: 10.1186/s12863-023-01164-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 10/09/2023] [Indexed: 10/28/2023] Open
Abstract
Canine anterior cruciate ligament (ACL) rupture is a common complex disease. Prevalence of ACL rupture is breed dependent. In an epidemiological study, yellow coat color was associated with increased risk of ACL rupture in the Labrador Retriever. ACL rupture risk variants may be linked to coat color through genetic selection or through linkage with coat color genes. To investigate these associations, Labrador Retrievers were phenotyped as ACL rupture case or controls and for coat color and were single nucleotide polymorphism (SNP) genotyped. After filtering, ~ 697 K SNPs were analyzed using GEMMA and mvBIMBAM for multivariate association. Functional annotation clustering analysis with DAVID was performed on candidate genes. A large 8 Mb region on chromosome 5 that included ACSF3, as well as 32 additional SNPs, met genome-wide significance at P < 6.07E-7 or Log10(BF) = 3.0 for GEMMA and mvBIMBAM, respectively. On chromosome 23, SNPs were located within or near PCCB and MSL2. On chromosome 30, a SNP was located within IGDCC3. SNPs associated with coat color were also located within ADAM9, FAM109B, SULT1C4, RTDR1, BCR, and RGS7. DZIP1L was associated with ACL rupture. Several significant SNPs on chromosomes 2, 3, 7, 24, and 26 were located within uncharacterized regions or long non-coding RNA sequences. This study validates associations with the previous ACL rupture candidate genes ACSF3 and DZIP1L and identifies novel candidate genes. These variants could act as targets for treatment or as factors in disease prediction modeling. The study highlighted the importance of regulatory SNPs in the disease, as several significant SNPs were located within non-coding regions.
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Affiliation(s)
- B T Lee
- Department of Surgical Sciences, University of Wisconsin-Madison, School of Veterinary Medicine, 2015 Linden Drive, Madison, WI, 53706, United States of America
| | - L A Baker
- Department of Surgical Sciences, University of Wisconsin-Madison, School of Veterinary Medicine, 2015 Linden Drive, Madison, WI, 53706, United States of America
| | - M Momen
- Department of Surgical Sciences, University of Wisconsin-Madison, School of Veterinary Medicine, 2015 Linden Drive, Madison, WI, 53706, United States of America
| | - H Terhaar
- Department of Surgical Sciences, University of Wisconsin-Madison, School of Veterinary Medicine, 2015 Linden Drive, Madison, WI, 53706, United States of America
| | - E E Binversie
- Department of Surgical Sciences, University of Wisconsin-Madison, School of Veterinary Medicine, 2015 Linden Drive, Madison, WI, 53706, United States of America
| | - S J Sample
- Department of Surgical Sciences, University of Wisconsin-Madison, School of Veterinary Medicine, 2015 Linden Drive, Madison, WI, 53706, United States of America
| | - Peter Muir
- Department of Surgical Sciences, University of Wisconsin-Madison, School of Veterinary Medicine, 2015 Linden Drive, Madison, WI, 53706, United States of America.
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Yang IS, Jang I, Yang JO, Choi J, Kim MS, Kim KK, Seung BJ, Cheong JH, Sur JH, Nam H, Lee B, Kim J, Kim S. CanISO: a database of genomic and transcriptomic variations in domestic dog (Canis lupus familiaris). BMC Genomics 2023; 24:613. [PMID: 37828501 PMCID: PMC10571338 DOI: 10.1186/s12864-023-09655-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 09/06/2023] [Indexed: 10/14/2023] Open
Abstract
BACKGROUND The domestic dog, Canis lupus familiaris, is a companion animal for humans as well as an animal model in cancer research due to similar spontaneous occurrence of cancers as humans. Despite the social and biological importance of dogs, the catalogue of genomic variations and transcripts for dogs is relatively incomplete. RESULTS We developed CanISO, a new database to hold a large collection of transcriptome profiles and genomic variations for domestic dogs. CanISO provides 87,692 novel transcript isoforms and 60,992 known isoforms from whole transcriptome sequencing of canine tumors (N = 157) and their matched normal tissues (N = 64). CanISO also provides genomic variation information for 210,444 unique germline single nucleotide polymorphisms (SNPs) from the whole exome sequencing of 183 dogs, with a query system that searches gene- and transcript-level information as well as covered SNPs. Transcriptome profiles can be compared with corresponding human transcript isoforms at a tissue level, or between sample groups to identify tumor-specific gene expression and alternative splicing patterns. CONCLUSIONS CanISO is expected to increase understanding of the dog genome and transcriptome, as well as its functional associations with humans, such as shared/distinct mechanisms of cancer. CanISO is publicly available at https://www.kobic.re.kr/caniso/ .
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Affiliation(s)
- In Seok Yang
- Department of Biomedical Systems Informatics, Yonsei University College of Medicine, Seoul, 03722, Korea
| | - Insu Jang
- Korea Bioinformation Center (KOBIC), Korea Research Institute of Bioscience & Biotechnology, Daejeon, 34141, Korea
| | - Jin Ok Yang
- Korea Bioinformation Center (KOBIC), Korea Research Institute of Bioscience & Biotechnology, Daejeon, 34141, Korea
| | - Jinhyuk Choi
- Korea Bioinformation Center (KOBIC), Korea Research Institute of Bioscience & Biotechnology, Daejeon, 34141, Korea
| | - Min-Seo Kim
- Korea Bioinformation Center (KOBIC), Korea Research Institute of Bioscience & Biotechnology, Daejeon, 34141, Korea
| | - Ka-Kyung Kim
- Department of Biomedical Systems Informatics, Yonsei University College of Medicine, Seoul, 03722, Korea
| | - Byung-Joon Seung
- Department of Veterinary Pathology, College of Veterinary Medicine, Konkuk University, Seoul, 05029, Korea
| | - Jae-Ho Cheong
- Department of Biomedical Systems Informatics, Yonsei University College of Medicine, Seoul, 03722, Korea
| | - Jung-Hyang Sur
- Department of Veterinary Pathology, College of Veterinary Medicine, Konkuk University, Seoul, 05029, Korea
| | - Hojung Nam
- School of Electrical Engineering and Computer Science, Gwangju Institute of Science and Technology (GIST), Gwangju, 61005, Korea
| | - Byungwook Lee
- Korea Bioinformation Center (KOBIC), Korea Research Institute of Bioscience & Biotechnology, Daejeon, 34141, Korea.
| | - Junho Kim
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Korea.
| | - Sangwoo Kim
- Department of Biomedical Systems Informatics, Yonsei University College of Medicine, Seoul, 03722, Korea.
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Leeb T. Special Issue: "Canine Genetics 2". Genes (Basel) 2023; 14:1930. [PMID: 37895280 PMCID: PMC10606197 DOI: 10.3390/genes14101930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 10/07/2023] [Indexed: 10/29/2023] Open
Abstract
Wolves were the first animal species to become domesticated by humans, approximately 30,000-50,000 years ago. Human-directed dog breeding over thousands of generations has generated more than 350 recognized breeds displaying surprisingly different phenotypes with respect to morphology, behavior and disease predispositions. The domestication of wolves and the subsequent breeding of dogs can be viewed as one of humankind's oldest and largest genetic experiments and provides us with unique opportunities for research. Dogs have not only become human's best friend but were also described as geneticists' best friend in a past issue of Science. In recognition of the importance of canine genetics, this Special Issue, entitled "Canine Genetics 2", was compiled. It represents a sequel to the former Special Issue "Canine Genetics", which was published in 2019. During the last 15 years, the canine community has heavily relied on a reference genome derived from the female Boxer Tasha. "Canine Genetics 2" includes an article describing a greatly improved version of this important community resource. This Special Issue further contains several reports related to monogenic or complex inherited diseases in dogs. Finally, important aspects of wild canid research, genetic diversity in different populations and canine morphology were investigated.
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Affiliation(s)
- Tosso Leeb
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001 Bern, Switzerland
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Kim K, Song JE, Joo JB, Park HA, Choi CH, Je CY, Kim OK, Park SW, Do YJ, Hur TY, Park SI, Lee CM. Genome-wide association study of mammary gland tumors in Maltese dogs. Front Vet Sci 2023; 10:1255981. [PMID: 37859946 PMCID: PMC10583716 DOI: 10.3389/fvets.2023.1255981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 09/19/2023] [Indexed: 10/21/2023] Open
Abstract
Background A genome-wide association study (GWAS) is a valuable tool for investigating genetic and phenotypic variation in many diseases. Objective The objective of this study was to identify variations in the genomes of Maltese dogs that are associated with the mammary gland tumor (MGT) phenotype and to assess the association between each biological condition and MGT phenotype in Maltese dogs. Methods DNA was extracted from 22 tumor samples and 11 whole blood samples from dogs with MGTs. Genome-wide single-nucleotide polymorphism (SNP) genotyping was performed, and the top 20 SNPs associated with various conditions and genetic variations were mapped to their corresponding gene locations. Results The genotyping process successfully identified 173,662 loci, with an overall genotype completion rate of 99.92%. Through the quality control analysis, 46,912 of these SNPs were excluded. Allelic tests were conducted to generate Manhattan plots, which showed several significant SNPs associated with MGT phenotype in intergenic region. The most prominent SNP, located within a region associated with transcription and linked to the malignancy grade of MGT, was identified on chromosome 5 (p = 0.00001) though there may be lack of statistical significance. Other SNPs were also found in several genes associated with oncogenesis, including TNFSF18, WDR3, ASIC5, STAR, and IL1RAP. Conclusion To our knowledge, this is the first GWAS to analyze the genetic predisposition to MGT in Maltese dogs. Despite the limited number of cases, these analyzed data could provide the basis for further research on the genetic predisposition to MGTs in Maltese dogs.
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Affiliation(s)
- Keon Kim
- Department of Veterinary Internal Medicine, College of Veterinary Medicine and BK21 FOUR Program, Chonnam National University, Gwangju, Republic of Korea
| | - Jung Eun Song
- Department of Veterinary Internal Medicine, College of Veterinary Medicine and BK21 FOUR Program, Chonnam National University, Gwangju, Republic of Korea
- Gwangju Animal Medical Center, Gwangju, Republic of Korea
| | - Jae Beom Joo
- Department of Veterinary Internal Medicine, College of Veterinary Medicine and BK21 FOUR Program, Chonnam National University, Gwangju, Republic of Korea
| | - Hyeon A Park
- Department of Veterinary Internal Medicine, College of Veterinary Medicine and BK21 FOUR Program, Chonnam National University, Gwangju, Republic of Korea
| | - Chang Hyeon Choi
- Department of Veterinary Internal Medicine, College of Veterinary Medicine and BK21 FOUR Program, Chonnam National University, Gwangju, Republic of Korea
| | - Chang Yun Je
- Department of Veterinary Internal Medicine, College of Veterinary Medicine and BK21 FOUR Program, Chonnam National University, Gwangju, Republic of Korea
| | - Ock Kyu Kim
- Department of Veterinary Internal Medicine, College of Veterinary Medicine and BK21 FOUR Program, Chonnam National University, Gwangju, Republic of Korea
| | - Sin Wook Park
- Department of Veterinary Internal Medicine, College of Veterinary Medicine and BK21 FOUR Program, Chonnam National University, Gwangju, Republic of Korea
| | - Yoon Jung Do
- Division of Animal Diseases and Health, National Institute of Animal Science, Rural Development Administration, Wanju-gun, Republic of Korea
| | - Tai-Young Hur
- Division of Animal Diseases and Health, National Institute of Animal Science, Rural Development Administration, Wanju-gun, Republic of Korea
| | - Sang-Ik Park
- Department of Veterinary Pathology, College of Veterinary Medicine and BK21 FOUR Program, Chonnam National University, Gwangju, Republic of Korea
| | - Chang-Min Lee
- Department of Veterinary Internal Medicine, College of Veterinary Medicine and BK21 FOUR Program, Chonnam National University, Gwangju, Republic of Korea
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Gu TT, Wu H, Yang F, Gaubert P, Heighton SP, Fu Y, Liu K, Luo SJ, Zhang HR, Hu JY, Yu L. Genomic analysis reveals a cryptic pangolin species. Proc Natl Acad Sci U S A 2023; 120:e2304096120. [PMID: 37748052 PMCID: PMC10556634 DOI: 10.1073/pnas.2304096120] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Accepted: 07/26/2023] [Indexed: 09/27/2023] Open
Abstract
Eight extant species of pangolins are currently recognized. Recent studies found that two mitochondrial haplotypes identified in confiscations in Hong Kong could not be assigned to any known pangolin species, implying the existence of a species. Here, we report that two additional mitochondrial haplotypes identified in independent confiscations from Yunnan align with the putative species haplotypes supporting the existence of this mysterious species/population. To verify the new species scenario we performed a comprehensive analysis of scale characteristics and 138 whole genomes representing all recognized pangolin species and the cryptic new species, 98 of which were generated here. Our morphometric results clearly attributed this cryptic species to Asian pangolins (Manis sp.) and the genomic data provide robust and compelling evidence that it is a pangolin species distinct from those recognized previously, which separated from the Philippine pangolin and Malayan pangolin over 5 Mya. Our study provides a solid genomic basis for its formal recognition as the ninth pangolin species or the fifth Asian one, supporting a new taxonomic classification of pangolins. The effects of glacial climate changes and recent anthropogenic activities driven by illegal trade are inferred to have caused its population decline with the genomic signatures showing low genetic diversity, a high level of inbreeding, and high genetic load. Our finding greatly expands current knowledge of pangolin diversity and evolution and has vital implications for conservation efforts to prevent the extinction of this enigmatic and endangered species from the wild.
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Affiliation(s)
- Tong-Tong Gu
- State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, School of Life Sciences, Yunnan University, Kunming650500, China
| | - Hong Wu
- State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, School of Life Sciences, Yunnan University, Kunming650500, China
| | - Feng Yang
- Kadoorie Farm and Botanic Garden, Tai Po, Hong Kong Special Administrative Region999077, China
| | - Philippe Gaubert
- Laboratoire Evolution et Diversité Biologique, Université Toulouse III–Paul Sabatier, 31062Toulouse Cedex 9, France
- Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Terminal de Cruzeiros do Porto de Leixões, Porto4450-208, Portugal
| | - Sean P. Heighton
- Laboratoire Evolution et Diversité Biologique, Université Toulouse III–Paul Sabatier, 31062Toulouse Cedex 9, France
| | - Yeyizhou Fu
- The State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing100871, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing100871, China
| | - Ke Liu
- The State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing100871, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing100871, China
| | - Shu-Jin Luo
- The State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing100871, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing100871, China
| | - Hua-Rong Zhang
- Kadoorie Farm and Botanic Garden, Tai Po, Hong Kong Special Administrative Region999077, China
| | - Jing-Yang Hu
- State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, School of Life Sciences, Yunnan University, Kunming650500, China
| | - Li Yu
- State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, School of Life Sciences, Yunnan University, Kunming650500, China
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47
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Preckler-Quisquater S, Kierepka EM, Reding DM, Piaggio AJ, Sacks BN. Can demographic histories explain long-term isolation and recent pulses of asymmetric gene flow between highly divergent grey fox lineages? Mol Ecol 2023; 32:5323-5337. [PMID: 37632719 DOI: 10.1111/mec.17105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 08/01/2023] [Accepted: 08/09/2023] [Indexed: 08/28/2023]
Abstract
Secondary contact zones between deeply divergent, yet interfertile, lineages provide windows into the speciation process. North American grey foxes (Urocyon cinereoargenteus) are divided into western and eastern lineages that diverged approximately 1 million years ago. These ancient lineages currently hybridize in a relatively narrow zone of contact in the southern Great Plains, a pattern more commonly observed in smaller-bodied taxa, which suggests relatively recent contact after a long period of allopatry. Based on local ancestry inference with whole-genome sequencing (n = 43), we identified two distinct Holocene pulses of admixture. The older pulse (500-3500 YBP) reflected unidirectional gene flow from east to west, whereas the more recent pulse (70-200 YBP) of admixture was bi-directional. Augmented with genotyping-by-sequencing data from 216 additional foxes, demographic analyses indicated that the eastern lineage declined precipitously after divergence, remaining small throughout most of the late Pleistocene, and expanding only during the Holocene. Genetic diversity in the eastern lineage was highest in the southeast and lowest near the contact zone, consistent with a westward expansion. Concordantly, distribution modelling indicated that during their isolation, the most suitable habitat occurred far east of today's contact zone or west of the Great Plains. Thus, long-term isolation was likely caused by the small, distant location of the eastern refugium, with recent contact reflecting a large increase in suitable habitat and corresponding demographic expansion from the eastern refugium. Ultimately, long-term isolation in grey foxes may reflect their specialized bio-climatic niche. This system presents an opportunity for future investigation of potential pre- and post-zygotic isolating mechanisms.
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Affiliation(s)
- Sophie Preckler-Quisquater
- Mammalian Ecology and Conservation Unit, Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis, California, USA
| | - Elizabeth M Kierepka
- North Carolina Museum of Natural Sciences, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, North Carolina, USA
| | - Dawn M Reding
- Department of Biology, Luther College, Decorah, Iowa, USA
| | - Antoinette J Piaggio
- USDA, Wildlife Services, National Wildlife Research Center, Wildlife Genetics Lab, Fort Collins, Colorado, USA
| | - Benjamin N Sacks
- Mammalian Ecology and Conservation Unit, Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis, California, USA
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, California, USA
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48
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Cichowska AW, Wisniewski J, Bromke MA, Olejnik B, Mogielnicka-Brzozowska M. Proteome Profiling of Canine Epididymal Fluid: In Search of Protein Markers of Epididymal Sperm Motility. Int J Mol Sci 2023; 24:14790. [PMID: 37834239 PMCID: PMC10573609 DOI: 10.3390/ijms241914790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 09/21/2023] [Accepted: 09/28/2023] [Indexed: 10/15/2023] Open
Abstract
Sperm maturation in the epididymis is based on interactions with proteins from epididymal fluid (EF). The aim of the study was to profile canine EF proteome and investigate correlations between EF protein content and epididymal spermatozoa (ES) motion parameters. Twenty-three male dogs were divided into two groups: good sperm motility (GSM) and poor sperm motility (PSM). The total motility and progressive motility differed significantly (p = 0.031; p < 0.001, respectively) between the GSM group and the PSM group. The semen samples were centrifuged to separate the EF apart from the ES. The canine EF proteins were analyzed using nano-liquid chromatography, which was coupled with quadrupole time-of-flight mass spectrometry (NanoUPLC-Q-TOF/MS) and bioinformatic tools for the first time. A total of 915 proteins were identified (GSM-506; PSM-409, respectively). UniProt identification resulted in six unique proteins (UPs) in the GSM group of dogs and four UPs in the PSM group. A semi-quantitative analysis showed a higher abundance (p < 0.05) of four differentially expressed proteins in the GSM group (ALB, CRISP2, LCNL1, PTGDS). Motility-dependent variations were detected in the EF proteome and were related to important metabolic pathways, which might suggest that several proteins could be potential ES motility biomarkers.
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Affiliation(s)
- Aleksandra W. Cichowska
- Department of Animal Biochemistry and Biotechnology, University of Warmia and Mazury in Olsztyn, Oczapowskiego 5, 10-719 Olsztyn, Poland
| | - Jerzy Wisniewski
- Department of Biochemistry, Molecular Biology and Biotechnology, Wroclaw University of Science and Technology, Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Mariusz A. Bromke
- Department of Biochemistry and Immunochemistry, Wroclaw Medical University, Chalubinskiego 10, 50-368 Wroclaw, Poland
| | - Beata Olejnik
- Department of Biochemistry and Immunochemistry, Wroclaw Medical University, Chalubinskiego 10, 50-368 Wroclaw, Poland
| | - Marzena Mogielnicka-Brzozowska
- Department of Animal Biochemistry and Biotechnology, University of Warmia and Mazury in Olsztyn, Oczapowskiego 5, 10-719 Olsztyn, Poland
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49
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Niskanen JE, Ohlsson Å, Ljungvall I, Drögemüller M, Ernst RF, Dooijes D, van Deutekom HWM, van Tintelen JP, Snijders Blok CJB, van Vugt M, van Setten J, Asselbergs FW, Petrič AD, Salonen M, Hundi S, Hörtenhuber M, Kere J, Pyle WG, Donner J, Postma AV, Leeb T, Andersson G, Hytönen MK, Häggström J, Wiberg M, Friederich J, Eberhard J, Harakalova M, van Steenbeek FG, Wess G, Lohi H. Identification of novel genetic risk factors of dilated cardiomyopathy: from canine to human. Genome Med 2023; 15:73. [PMID: 37723491 PMCID: PMC10506233 DOI: 10.1186/s13073-023-01221-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 08/17/2023] [Indexed: 09/20/2023] Open
Abstract
BACKGROUND Dilated cardiomyopathy (DCM) is a life-threatening heart disease and a common cause of heart failure due to systolic dysfunction and subsequent left or biventricular dilatation. A significant number of cases have a genetic etiology; however, as a complex disease, the exact genetic risk factors are largely unknown, and many patients remain without a molecular diagnosis. METHODS We performed GWAS followed by whole-genome, transcriptome, and immunohistochemical analyses in a spontaneously occurring canine model of DCM. Canine gene discovery was followed up in three human DCM cohorts. RESULTS Our results revealed two independent additive loci associated with the typical DCM phenotype comprising left ventricular systolic dysfunction and dilatation. We highlight two novel candidate genes, RNF207 and PRKAA2, known for their involvement in cardiac action potentials, energy homeostasis, and morphology. We further illustrate the distinct genetic etiologies underlying the typical DCM phenotype and ventricular premature contractions. Finally, we followed up on the canine discoveries in human DCM patients and discovered candidate variants in our two novel genes. CONCLUSIONS Collectively, our study yields insight into the molecular pathophysiology of DCM and provides a large animal model for preclinical studies.
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Affiliation(s)
- Julia E Niskanen
- Department of Medical and Clinical Genetics, University of Helsinki, Haartmaninkatu 8, 00290, Helsinki, Finland
- Department of Veterinary Biosciences, University of Helsinki, Agnes Sjöbergin katu 2, 00790, Helsinki, Finland
- Folkhälsan Research Center, Haartmaninkatu 8, P.O.Box 63, 00290, Helsinki, Finland
| | - Åsa Ohlsson
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Ingrid Ljungvall
- Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Michaela Drögemüller
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, 3001, Switzerland
| | - Robert F Ernst
- Department of Genetics, University Medical Centre Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Dennis Dooijes
- Department of Genetics, University Medical Centre Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Hanneke W M van Deutekom
- Department of Genetics, University Medical Centre Utrecht, Utrecht University, Utrecht, The Netherlands
| | - J Peter van Tintelen
- Department of Genetics, University Medical Centre Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Christian J B Snijders Blok
- Department of Cardiology, Division Heart & Lungs, University Medical Center Utrecht (UMCU), Utrecht, The Netherlands
- Regenerative Medicine Centre Utrecht, University of Utrecht, Utrecht, The Netherlands
| | - Marion van Vugt
- Department of Cardiology, Division Heart & Lungs, University Medical Center Utrecht (UMCU), Utrecht, The Netherlands
| | - Jessica van Setten
- Department of Cardiology, Division Heart & Lungs, University Medical Center Utrecht (UMCU), Utrecht, The Netherlands
| | - Folkert W Asselbergs
- Amsterdam University Medical Centers, Department of Cardiology, University of Amsterdam, Amsterdam, The Netherlands
- Health Data Research UK and Institute of Health Informatics, University College London, London, UK
| | | | - Milla Salonen
- Department of Medical and Clinical Genetics, University of Helsinki, Haartmaninkatu 8, 00290, Helsinki, Finland
- Department of Veterinary Biosciences, University of Helsinki, Agnes Sjöbergin katu 2, 00790, Helsinki, Finland
- Folkhälsan Research Center, Haartmaninkatu 8, P.O.Box 63, 00290, Helsinki, Finland
| | - Sruthi Hundi
- Department of Medical and Clinical Genetics, University of Helsinki, Haartmaninkatu 8, 00290, Helsinki, Finland
- Department of Veterinary Biosciences, University of Helsinki, Agnes Sjöbergin katu 2, 00790, Helsinki, Finland
- Folkhälsan Research Center, Haartmaninkatu 8, P.O.Box 63, 00290, Helsinki, Finland
| | - Matthias Hörtenhuber
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Juha Kere
- Folkhälsan Research Center, Haartmaninkatu 8, P.O.Box 63, 00290, Helsinki, Finland
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
- Research Programs Unit, Stem Cells and Metabolism Research Program, University of Helsinki, Helsinki, Finland
| | - W Glen Pyle
- Department of Biomedical Sciences, University of Guelph, Guelph, ON, Canada
- IMPART Investigator Team Canada, Dalhousie Medicine, Saint John, NB, Canada
| | - Jonas Donner
- Wisdom Panel Research Team, Wisdom Panel, Kinship, Helsinki, Finland
| | - Alex V Postma
- Department of Human Genetics, Amsterdam University Medical Center, Amsterdam, The Netherlands
- Department of Medical Biology, Amsterdam University Medical Center, Amsterdam, The Netherlands
| | - Tosso Leeb
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, 3001, Switzerland
| | - Göran Andersson
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Marjo K Hytönen
- Department of Medical and Clinical Genetics, University of Helsinki, Haartmaninkatu 8, 00290, Helsinki, Finland
- Department of Veterinary Biosciences, University of Helsinki, Agnes Sjöbergin katu 2, 00790, Helsinki, Finland
- Folkhälsan Research Center, Haartmaninkatu 8, P.O.Box 63, 00290, Helsinki, Finland
| | - Jens Häggström
- Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Maria Wiberg
- Department of Equine and Small Animal Medicine, University of Helsinki, Helsinki, Finland
| | - Jana Friederich
- LMU Small Animal Clinic, Ludwig Maximilians University of Munich, Munich, Germany
| | - Jenny Eberhard
- LMU Small Animal Clinic, Ludwig Maximilians University of Munich, Munich, Germany
| | - Magdalena Harakalova
- Department of Cardiology, Division Heart & Lungs, University Medical Center Utrecht (UMCU), Utrecht, The Netherlands
- Regenerative Medicine Centre Utrecht, University of Utrecht, Utrecht, The Netherlands
| | - Frank G van Steenbeek
- Department of Cardiology, Division Heart & Lungs, University Medical Center Utrecht (UMCU), Utrecht, The Netherlands
- Regenerative Medicine Centre Utrecht, University of Utrecht, Utrecht, The Netherlands
- Department of Clinical Sciences, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 108, Utrecht, 3584 CM, The Netherlands
| | - Gerhard Wess
- LMU Small Animal Clinic, Ludwig Maximilians University of Munich, Munich, Germany
| | - Hannes Lohi
- Department of Medical and Clinical Genetics, University of Helsinki, Haartmaninkatu 8, 00290, Helsinki, Finland.
- Department of Veterinary Biosciences, University of Helsinki, Agnes Sjöbergin katu 2, 00790, Helsinki, Finland.
- Folkhälsan Research Center, Haartmaninkatu 8, P.O.Box 63, 00290, Helsinki, Finland.
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50
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Sheikh MM, Tak H, Fazili MF, Wani IN. A coprological survey on helminths of Jackal Canis aureus Linnaeus 1758 in Kashmir Himalaya. J Parasit Dis 2023; 47:491-500. [PMID: 37520190 PMCID: PMC10382462 DOI: 10.1007/s12639-023-01588-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 04/14/2023] [Indexed: 08/01/2023] Open
Abstract
A coprological examination was carried out between February 2017 and January 2019 to determine the prevalence of gastrointestinal helminths in jackals of Kashmir Himalaya, India. Fecal floatation and sedimentation technique revealed helminths in 215 scats out of 879 examined scats, with overall helminth prevalence of 24.45%. In the study, five different species of helminths were detected in scats of jackal: Toxocara canis (22.86%), Ancylostoma caninum (20.47%), Dipylidium caninum (17.17%), Trichuris vulpis (19.34%), and taeniid eggs (13.65%). One helminth species was found in (0.11%) of the jackal scats, two were in (1.25%), three were in (4.77%), four were in (16.38%), and five were in (1.92%). Toxocara canis, a nematode with great zoonotic significance, was most common helminth found in scats of jackal during the study. We observed significant seasonal fluctuation (p < 0.05) in the prevalence of gastrointestinal helminths, with summer having high frequency followed by autumn, spring, and winter having lowest prevalence. The study area's jackal population's preponderance of zoonotic helminth species suggests a high risk of zoonotic infection by canine intestinal helminths. This study will aid veterinarians in better plan preventative strategies with regard to wild animal intestinal parasites.
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Affiliation(s)
- Mohmad Muzafar Sheikh
- Parasitology Research Laboratory, Department of Zoology, University of Kashmir, Srinagar, Jammu and Kashmir 190006 India
| | - Hidayatullah Tak
- Parasitology Research Laboratory, Department of Zoology, University of Kashmir, Srinagar, Jammu and Kashmir 190006 India
| | - Mustahson F. Fazili
- Biodviersity Conservation Laboratory, Department of Zoology, University of Kashmir, Srinagar, Jammu and Kashmir 190006 India
| | - Ishfaq Nazir Wani
- Biodviersity Conservation Laboratory, Department of Zoology, University of Kashmir, Srinagar, Jammu and Kashmir 190006 India
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